diff --git a/NAMESPACE b/NAMESPACE
index c41b675..a1432df 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -11,14 +11,14 @@ export(adjustEnrichment)
 export(aggHicMatrices)
 export(aggMetadata)
 export(as_ginteractions)
-export(assignToBins)
+export(binPairs)
 export(binRanges)
 export(calcLoopEnrichment)
 export(changePixelRes)
-export(clusters)
 export(defaultBuffer)
 export(end1)
 export(end2)
+export(getPairClusters)
 export(hdf5BlockApply)
 export(makeGInteractionsFromDataFrame)
 export(makeRandomGInteractions)
@@ -52,12 +52,12 @@ export(selectTopRight)
 export(selectionMethod)
 export(seqnames1)
 export(seqnames2)
-export(sets)
 export(shiftRanges)
 export(snapToBins)
 export(sources)
 export(start1)
 export(start2)
+export(subsetBySource)
 exportClasses(DelegatingGInteractions)
 exportClasses(InteractionArray)
 exportClasses(InteractionJaggedArray)
@@ -79,12 +79,11 @@ exportMethods(aggHicMatrices)
 exportMethods(aggMetadata)
 exportMethods(as.list)
 exportMethods(as_ginteractions)
-exportMethods(assignToBins)
+exportMethods(binPairs)
 exportMethods(binRanges)
 exportMethods(calcLoopEnrichment)
 exportMethods(cbind)
 exportMethods(changePixelRes)
-exportMethods(clusters)
 exportMethods(colData)
 exportMethods(countOverlaps)
 exportMethods(counts)
@@ -92,6 +91,7 @@ exportMethods(dim)
 exportMethods(end1)
 exportMethods(end2)
 exportMethods(findOverlaps)
+exportMethods(getPairClusters)
 exportMethods(hdf5BlockApply)
 exportMethods(interactions)
 exportMethods(length)
@@ -131,7 +131,6 @@ exportMethods(selectTopRight)
 exportMethods(selectionMethod)
 exportMethods(seqnames1)
 exportMethods(seqnames2)
-exportMethods(sets)
 exportMethods(shiftRanges)
 exportMethods(show)
 exportMethods(snapToBins)
@@ -139,6 +138,7 @@ exportMethods(sources)
 exportMethods(start1)
 exportMethods(start2)
 exportMethods(subsetByOverlaps)
+exportMethods(subsetBySource)
 import(data.table,
  except = c(between, shift, first, second, indices))
 import(methods)
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index 0009ff4..c7b3367 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -16,15 +16,15 @@ setGeneric("makeGInteractionsFromDataFrame",
                     ...)
                standardGeneric("makeGInteractionsFromDataFrame"))
 
-#' @rdname assignToBins
+#' @rdname binPairs
 #' @export
-setGeneric("assignToBins",
+setGeneric("binPairs",
            function(x,
                     binSize,
                     pos1 = 'center',
                     pos2 = 'center',
                     ...)
-               standardGeneric("assignToBins"))
+               standardGeneric("binPairs"))
 
 #' @rdname binRanges
 #' @export
@@ -63,22 +63,22 @@ setGeneric("mergePairs",
 setGeneric("selectionMethod", function(x, ...)
     standardGeneric("selectionMethod"))
 
-#' @rdname clusters
+#' @rdname getPairClusters
 #' @export
-setGeneric("clusters", function(x, ...)
-    standardGeneric("clusters"))
+setGeneric("getPairClusters", function(x, ...)
+    standardGeneric("getPairClusters"))
 
 #' @rdname sources
 #' @export
 setGeneric("sources", function(x)
     standardGeneric("sources"))
 
-#' @rdname sets
+#' @rdname subsetBySource
 #' @export
-setGeneric("sets", function(x,
+setGeneric("subsetBySource", function(x,
                                       include,
                                       exclude)
-    standardGeneric("sets"))
+    standardGeneric("subsetBySource"))
 
 #' @rdname aggMetadata
 #' @export
diff --git a/R/methods-CountMatrix.R b/R/methods-CountMatrix.R
index 39745a7..f63fbae 100644
--- a/R/methods-CountMatrix.R
+++ b/R/methods-CountMatrix.R
@@ -35,7 +35,7 @@
 #'     setNames("WT") |>
 #'     read.table(header=TRUE) |>
 #'     as_ginteractions(keep.extra.columns=FALSE) |>
-#'     assignToBins(binSize=100e3)
+#'     binPairs(binSize=100e3)
 #'
 #' ## Removes the "chr" prefix for compatibility
 #' ## with the preprocessed hic files
diff --git a/R/methods-InteractionJaggedArray.R b/R/methods-InteractionJaggedArray.R
index 1196d57..df0cb94 100644
--- a/R/methods-InteractionJaggedArray.R
+++ b/R/methods-InteractionJaggedArray.R
@@ -303,7 +303,7 @@ setMethod("[", "InteractionJaggedArray", function(x, i, j) {
 #' iarr <- pullHicMatrices(gi, hicFiles, 100e03, half="both")
 #'
 #' ## Shift first two ranges out of range
-#' gi2 <- c(assignToBins(gi[1:2], binSize=100e3, pos1=-200e3), gi[3:4])
+#' gi2 <- c(binPairs(gi[1:2], binSize=100e3, pos1=-200e3), gi[3:4])
 #'
 #' ## Find overlaps
 #' findOverlaps(iarr, gi2)
diff --git a/R/methods-MatrixSelection.R b/R/methods-MatrixSelection.R
index 1203be2..d500d9d 100644
--- a/R/methods-MatrixSelection.R
+++ b/R/methods-MatrixSelection.R
@@ -38,7 +38,7 @@
         abort(c(glue("All interactions in `x` must be \\
                      the same width."),
                 "i"="Check this with `width(x)`.",
-                "i"="Set binSize with `assignToBins(x, binSize)`."))
+                "i"="Set binSize with `binPairs(x, binSize)`."))
     }
     ## How does moving down or right change dist to diag?
     p <- pairdist(x)
diff --git a/R/methods-MergedGInteractions.R b/R/methods-MergedGInteractions.R
index 9932117..5362a3f 100644
--- a/R/methods-MergedGInteractions.R
+++ b/R/methods-MergedGInteractions.R
@@ -162,7 +162,7 @@ setMethod("aggMetadata", signature(x = "MergedGInteractions",
 #' Access the names or source files of
 #' a `MergedGInteractions` object.
 #'
-#' @inheritParams sets
+#' @inheritParams subsetBySource
 #' @return A character vector of names or source
 #'  files of a `MergedGInteractions` object.
 #' @examples
@@ -198,7 +198,7 @@ setMethod("sources", "MergedGInteractions",
           function(x) as.character(unique(x@allPairs$src)))
 
 #' Create logial matrix of sources for each merged pair
-#' @inheritParams sets
+#' @inheritParams subsetBySource
 #' @importFrom data.table data.table as.data.table
 #' @importFrom stats setNames
 #' @return A logical matrix with columns for each source
@@ -241,7 +241,7 @@ setMethod("sources", "MergedGInteractions",
 }
 
 #' Check source names
-#' @inheritParams sets
+#' @inheritParams subsetBySource
 #' @param vec Input character vector (i.e. include, exclude or both)
 #' @importFrom glue glue glue_collapse double_quote
 #' @importFrom rlang abort
@@ -264,11 +264,11 @@ setMethod("sources", "MergedGInteractions",
 }
 
 #' Find subset pairs using include and exclude sources
-#' @inheritParams sets
+#' @inheritParams subsetBySource
 #' @importFrom data.table data.table
 #' @return A `MergedGInteractions` object of subset pairs.
 #' @noRd
-.setsIncludeExclude <- function(x, include, exclude) {
+.subsetBySourceIncludeExclude <- function(x, include, exclude) {
 
     ## Check source names
     .checkSourceNames(x, vec = c(include, exclude))
@@ -286,11 +286,11 @@ setMethod("sources", "MergedGInteractions",
 }
 
 #' Find subset pairs using include sources
-#' @inheritParams sets
+#' @inheritParams subsetBySource
 #' @importFrom data.table data.table
 #' @return A `MergedGInteractions` object of subset pairs.
 #' @noRd
-.setsInclude <- function(x, include) {
+.subsetBySourceInclude <- function(x, include) {
 
     ## Check source names
     .checkSourceNames(x, vec = include)
@@ -306,11 +306,11 @@ setMethod("sources", "MergedGInteractions",
 }
 
 #' Find subset pairs using exclude sources
-#' @inheritParams sets
+#' @inheritParams subsetBySource
 #' @importFrom data.table data.table
 #' @return A `MergedGInteractions` object of subset pairs.
 #' @noRd
-.setsExclude <- function(x, exclude) {
+.subsetBySourceExclude <- function(x, exclude) {
 
     ## Check source names
     .checkSourceNames(x, vec = exclude)
@@ -331,7 +331,7 @@ setMethod("sources", "MergedGInteractions",
 #' @importFrom utils combn
 #' @return A `MergedGInteractions` object of de novo pairs.
 #' @noRd
-.sets <- function(x) {
+.subsetBySource <- function(x) {
     
     ## Calculate the src matrix
     srcMat <- .makeSrcMatrix(x)
@@ -374,9 +374,9 @@ setMethod("sources", "MergedGInteractions",
     }) |> unlist()
     names(idxList) <- srcNames
     
-    ## Index the sets
-    sets <- lapply(idxList, \(i) x[i])
-    return(sets)
+    ## Index the subsetBySource
+    subsetBySource <- lapply(idxList, \(i) x[i])
+    return(subsetBySource)
 }
 
 #' Get each set from a MergedGInteractions object
@@ -389,8 +389,8 @@ setMethod("sources", "MergedGInteractions",
 #' merged pair is not returned.
 #'
 #' Optional `include` and `exclude` parameters modulate
-#' the behavior of `sets` to return different
-#' subsets of originating pairs. For example, `include` requires
+#' the behavior of `subsetBySource` to return different
+#' subsubsetBySource of originating pairs. For example, `include` requires
 #' that the returned pairs be present in specific sources,
 #' while `exclude` requires that returned pairs be absent
 #' from specific sources. Sources not listed in either
@@ -435,47 +435,47 @@ setMethod("sources", "MergedGInteractions",
 #' ## Merge pairs
 #' x <- mergePairs(x = giList, radius = 20)
 #'
-#' sets(x)
+#' subsetBySource(x)
 #'
-#' @rdname sets
+#' @rdname subsetBySource
 #' @export
-setMethod("sets",
+setMethod("subsetBySource",
           signature(x = "MergedGInteractions",
                     include = "missing",
                     exclude = "missing"),
-          definition = .sets)
+          definition = .subsetBySource)
 
-#' @rdname sets
+#' @rdname subsetBySource
 #' @export
-setMethod("sets",
+setMethod("subsetBySource",
           signature(x = "MergedGInteractions",
                     include = "character_OR_missing",
                     exclude = "missing"),
-          definition = .setsInclude)
+          definition = .subsetBySourceInclude)
 
-#' @rdname sets
+#' @rdname subsetBySource
 #' @export
-setMethod("sets",
+setMethod("subsetBySource",
           signature(x = "MergedGInteractions",
                     include = "missing",
                     exclude = "character_OR_missing"),
-          definition = .setsExclude)
+          definition = .subsetBySourceExclude)
 
-#' @rdname sets
+#' @rdname subsetBySource
 #' @export
-setMethod("sets",
+setMethod("subsetBySource",
           signature(x = "MergedGInteractions",
                     include = "character_OR_missing",
                     exclude = "character_OR_missing"),
-          definition = .setsIncludeExclude)
+          definition = .subsetBySourceIncludeExclude)
 
 
 
-#' Internal accessor function for clusters
-#' @inheritParams clusters
+#' Internal accessor function for getPairClusters
+#' @inheritParams getPairClusters
 #' @importFrom data.table data.table
 #' @noRd
-.clusters <- function(x) {
+.getPairClusters <- function(x) {
 
     ## Suppress NSE notes in R CMD check
     i.id <- NULL
@@ -533,16 +533,16 @@ setMethod("sets",
 #'                 radius = 10e03,
 #'                 column = "APScoreAvg")
 #'
-#' ## Access pair clusters
-#' clusters(x[1:3])
-#' clusters(x[3:1])
-#' clusters(x[c(3, 1, 2)])
-#' clusters(x) |> length()
+#' ## Access pair getPairClusters
+#' getPairClusters(x[1:3])
+#' getPairClusters(x[3:1])
+#' getPairClusters(x[c(3, 1, 2)])
+#' getPairClusters(x) |> length()
 #'
-#' @rdname clusters
+#' @rdname getPairClusters
 #' @export
-setMethod("clusters", signature(x = "MergedGInteractions"),
-          definition = .clusters)
+setMethod("getPairClusters", signature(x = "MergedGInteractions"),
+          definition = .getPairClusters)
 
 #' Get selectionMethod from MergedGInteractions object
 #'
diff --git a/R/methods-adjustEnrichment.R b/R/methods-adjustEnrichment.R
index 767c074..dc44016 100644
--- a/R/methods-adjustEnrichment.R
+++ b/R/methods-adjustEnrichment.R
@@ -122,7 +122,7 @@
 #'
 #' ## Calculate loop enrichment
 #' enrich <- calcLoopEnrichment(
-#'     x=assignToBins(loops, 100e03),
+#'     x=binPairs(loops, 100e03),
 #'     files=hicFiles
 #' )
 #'
diff --git a/R/methods-aggHicMatrices.R b/R/methods-aggHicMatrices.R
index 701927d..0094fec 100644
--- a/R/methods-aggHicMatrices.R
+++ b/R/methods-aggHicMatrices.R
@@ -229,7 +229,7 @@
 #'
 #' ## Expand pixel ranges with a 5 pixel buffer on either side
 #' loops <-
-#'     assignToBins(loops, binSize=100e3) |>
+#'     binPairs(loops, binSize=100e3) |>
 #'     pixelsToMatrices(buffer=5)
 #'
 #' ## Extract 10, 11x11 count matrices from 2 hic files
diff --git a/R/methods-assignToBins.R b/R/methods-assignToBins.R
index 56dbd6b..6fb6177 100644
--- a/R/methods-assignToBins.R
+++ b/R/methods-assignToBins.R
@@ -1,5 +1,5 @@
-#' Internal assignToBins function
-#' @inheritParams assignToBins
+#' Internal binPairs function
+#' @inheritParams binPairs
 #' @importFrom data.table data.table
 #' @importFrom S4Vectors DataFrame mcols
 #' @importFrom InteractionSet anchors
@@ -7,7 +7,7 @@
 #' @return Input object that has been binned.
 #'
 #' @noRd
-.assignToBins <- function(x, binSize, pos1, pos2) {
+.binPairs <- function(x, binSize, pos1, pos2) {
 
     ## Convert x to a GInteractions
     if (is(x, 'data.frame') | is(x, 'DFrame')) {
@@ -73,21 +73,21 @@
 #'                chr2 = "chr1", y1 = 30000, y2 = 40000)
 #'
 #' ## Assign each range to 20-kb bins from the start positions
-#' assignToBins(x = df1,
+#' binPairs(x = df1,
 #'          binSize = 20000,
 #'          pos1 = 'start',
 #'          pos2 = 'start')
 #'
-#' @rdname assignToBins
+#' @rdname binPairs
 #' @export
-setMethod("assignToBins",
+setMethod("binPairs",
           signature(x = 'DF_OR_df_OR_dt',
                     binSize = 'numeric',
                     pos1 = 'character_OR_numeric_OR_missing',
                     pos2 = 'character_OR_numeric_OR_missing'),
-          definition = .assignToBins)
+          definition = .binPairs)
 
-#' @rdname assignToBins
+#' @rdname binPairs
 #' @examples
 #' ## Construct GInteractions
 #' library(InteractionSet)
@@ -97,14 +97,14 @@ setMethod("assignToBins",
 #'     as_ginteractions()
 #'
 #' ## Assign each range to 20-kb bins from the start positions
-#' assignToBins(x = gi1,
+#' binPairs(x = gi1,
 #'          binSize = 20000,
 #'          pos1 = 'start',
 #'          pos2 = 'start')
 #' @export
-setMethod("assignToBins",
+setMethod("binPairs",
           signature(x = 'GInteractions',
                     binSize = 'numeric',
                     pos1 = 'character_OR_numeric_OR_missing',
                     pos2 = 'character_OR_numeric_OR_missing'),
-          definition = .assignToBins)
+          definition = .binPairs)
diff --git a/R/methods-calcLoopEnrichment.R b/R/methods-calcLoopEnrichment.R
index 24ce597..72f9019 100644
--- a/R/methods-calcLoopEnrichment.R
+++ b/R/methods-calcLoopEnrichment.R
@@ -138,7 +138,7 @@
     abort(c(glue("All interactions in `x` must be \\
                      the same width."),
             "i"="Check this with `width(x)`.",
-            "i"="Set binSize with `assignToBins(x, binSize)`."))
+            "i"="Set binSize with `binPairs(x, binSize)`."))
   }
   
   ## Check & show selection
@@ -266,7 +266,7 @@
 #' GenomeInfoDb::seqlevelsStyle(loops) <- 'ENSEMBL'
 #'
 #' ## Expand binSize of loops
-#' loops <- assignToBins(x=loops, binSize=100e3)
+#' loops <- binPairs(x=loops, binSize=100e3)
 #'
 #' ## Calculate loop enrichment
 #' calcLoopEnrichment(x=loops[1:10],
@@ -296,7 +296,7 @@ setMethod("calcLoopEnrichment",
 #'
 #' @examples
 #' ## Extract count matrices first
-#' mats <- assignToBins(loops[1:10],100e3) |>
+#' mats <- binPairs(loops[1:10],100e3) |>
 #'   pixelsToMatrices(buffer=10) |>
 #'     pullHicMatrices(
 #'     files=hicFiles,
diff --git a/R/methods-changePixelRes.R b/R/methods-changePixelRes.R
index 3734c99..1e6d389 100644
--- a/R/methods-changePixelRes.R
+++ b/R/methods-changePixelRes.R
@@ -113,7 +113,7 @@
 #' GenomeInfoDb::seqlevelsStyle(loops) <- 'ENSEMBL'
 #'
 #' ## Rebin loops to 2.5e6 resolution
-#' loops <- assignToBins(x=loops, binSize=2.5e06)
+#' loops <- binPairs(x=loops, binSize=2.5e06)
 #'
 #' ## Pull 5x5 matrices
 #' iarr <- pullHicMatrices(x=loops[1:5],
@@ -155,7 +155,7 @@ setMethod("selectPixel",
 
     ## Execute steps
     x |>
-        assignToBins(binSize=from) |>
+        binPairs(binSize=from) |>
         pullHicMatrices(binSize=to, files=files, norm=norm, ...) |>
         selectPixel(aggFUN, selectFUN, nBlocks, verbose)
 }
@@ -237,7 +237,7 @@ setMethod("selectPixel",
 #' GenomeInfoDb::seqlevelsStyle(loops) <- 'ENSEMBL'
 #'
 #' ## Rebin loops to 2.5e6 resolution
-#' loops <- assignToBins(x=loops, binSize=2.5e06)
+#' loops <- binPairs(x=loops, binSize=2.5e06)
 #'
 #' ## Change pixel resolution from 2.5e6 to 500e3
 #' changePixelRes(x=loops[1:5],
diff --git a/R/methods-pileupPixels.R b/R/methods-pileupPixels.R
index 086b2af..09776d5 100644
--- a/R/methods-pileupPixels.R
+++ b/R/methods-pileupPixels.R
@@ -91,7 +91,7 @@
 #'     setNames("WT") |>
 #'     read.table(header=TRUE, nrows=1000) |>
 #'     as_ginteractions(keep.extra.columns=FALSE) |>
-#'     assignToBins(binSize=5e3)
+#'     binPairs(binSize=5e3)
 #' 
 #' ## Removes the "chr" prefix for compatibility
 #' ## with the preprocessed hic files
diff --git a/R/methods-pullHic.R b/R/methods-pullHic.R
index 4013577..50a61b6 100644
--- a/R/methods-pullHic.R
+++ b/R/methods-pullHic.R
@@ -43,7 +43,7 @@
         x <- snapToBins(x, binSize)
         msg <- c("Pairs are not binned to `binSize`.",
                  'i' = glue("Snapping to binSize={binSize}, "),
-                 'i' = glue("Use `assignToBins()` or `snapToBins()` ",
+                 'i' = glue("Use `binPairs()` or `snapToBins()` ",
                             "for more binning options."))
         inform(msg)
     }
@@ -873,7 +873,7 @@
 #'   setNames("WT") |>
 #'   read.table(header=TRUE) |>
 #'   as_ginteractions(keep.extra.columns=FALSE) |>
-#'   assignToBins(binSize=100e3)
+#'   binPairs(binSize=100e3)
 #'
 #' ## Removes the "chr" prefix for compatibility
 #' ## with the preprocessed hic files
@@ -1097,7 +1097,7 @@ setMethod("pullHicMatrices",
         abort(c("`x` are not binned to `binSize`.",
                 'i' = glue("All ranges in `x` must be equal \\
                            widths for `pullHicPixels()`."),
-                'i' = glue("Use `assignToBins()` to bin or use \\
+                'i' = glue("Use `binPairs()` to bin or use \\
                            `pullHicMatrices()` instead.")))
     }
 
@@ -1184,7 +1184,7 @@ setMethod("pullHicMatrices",
 #'   setNames("WT") |>
 #'   read.table(header=TRUE) |>
 #'   as_ginteractions(keep.extra.columns=FALSE) |>
-#'   assignToBins(binSize=100e3)
+#'   binPairs(binSize=100e3)
 #'
 #' ## Removes the "chr" prefix for compatibility
 #' ## with the preprocessed hic files
diff --git a/R/utils.R b/R/utils.R
index db15a49..7476814 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -227,7 +227,7 @@
   widths <- unique(width(regions(x))) - 1
   if (length(widths) != 1L) {
     abort(c("All ranges in `x` must be equal widths.",
-            "i"="Use `assignToBins()` to bin into equal widths."))
+            "i"="Use `binPairs()` to bin into equal widths."))
   }
   return(widths)
 }
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 7ec7cda..d000a63 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -18,7 +18,7 @@ reference:
       - as_ginteractions
       - shiftRanges
       - binRanges
-      - assignToBins
+      - binPairs
       - snapToBins
       - seqnames1
       - makeRandomGRanges
diff --git a/man/CountMatrix-class.Rd b/man/CountMatrix-class.Rd
index f5638ef..fde6871 100644
--- a/man/CountMatrix-class.Rd
+++ b/man/CountMatrix-class.Rd
@@ -51,7 +51,7 @@ pixels <-
     setNames("WT") |>
     read.table(header=TRUE) |>
     as_ginteractions(keep.extra.columns=FALSE) |>
-    assignToBins(binSize=100e3)
+    binPairs(binSize=100e3)
 
 ## Removes the "chr" prefix for compatibility
 ## with the preprocessed hic files
diff --git a/man/InteractionJaggedArray-overlaps.Rd b/man/InteractionJaggedArray-overlaps.Rd
index 77c404e..26a0dee 100644
--- a/man/InteractionJaggedArray-overlaps.Rd
+++ b/man/InteractionJaggedArray-overlaps.Rd
@@ -212,7 +212,7 @@ gi <- read.table(text="
 iarr <- pullHicMatrices(gi, hicFiles, 100e03, half="both")
 
 ## Shift first two ranges out of range
-gi2 <- c(assignToBins(gi[1:2], binSize=100e3, pos1=-200e3), gi[3:4])
+gi2 <- c(binPairs(gi[1:2], binSize=100e3, pos1=-200e3), gi[3:4])
 
 ## Find overlaps
 findOverlaps(iarr, gi2)
diff --git a/man/adjustEnrichment.Rd b/man/adjustEnrichment.Rd
index facc406..7362cad 100644
--- a/man/adjustEnrichment.Rd
+++ b/man/adjustEnrichment.Rd
@@ -72,7 +72,7 @@ GenomeInfoDb::seqlevelsStyle(loops) <- 'ENSEMBL'
 
 ## Calculate loop enrichment
 enrich <- calcLoopEnrichment(
-    x=assignToBins(loops, 100e03),
+    x=binPairs(loops, 100e03),
     files=hicFiles
 )
 
diff --git a/man/aggHicMatrices.Rd b/man/aggHicMatrices.Rd
index 7bb4763..c80da37 100644
--- a/man/aggHicMatrices.Rd
+++ b/man/aggHicMatrices.Rd
@@ -101,7 +101,7 @@ GenomeInfoDb::seqlevelsStyle(loops) <- 'ENSEMBL'
 
 ## Expand pixel ranges with a 5 pixel buffer on either side
 loops <-
-    assignToBins(loops, binSize=100e3) |>
+    binPairs(loops, binSize=100e3) |>
     pixelsToMatrices(buffer=5)
 
 ## Extract 10, 11x11 count matrices from 2 hic files
diff --git a/man/assignToBins.Rd b/man/binPairs.Rd
similarity index 71%
rename from man/assignToBins.Rd
rename to man/binPairs.Rd
index a86801a..25ad679 100644
--- a/man/assignToBins.Rd
+++ b/man/binPairs.Rd
@@ -1,16 +1,16 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/AllGenerics.R, R/methods-assignToBins.R
-\name{assignToBins}
-\alias{assignToBins}
-\alias{assignToBins,DF_OR_df_OR_dt,numeric,character_OR_numeric_OR_missing,character_OR_numeric_OR_missing-method}
-\alias{assignToBins,GInteractions,numeric,character_OR_numeric_OR_missing,character_OR_numeric_OR_missing-method}
+\name{binPairs}
+\alias{binPairs}
+\alias{binPairs,DF_OR_df_OR_dt,numeric,character_OR_numeric_OR_missing,character_OR_numeric_OR_missing-method}
+\alias{binPairs,GInteractions,numeric,character_OR_numeric_OR_missing,character_OR_numeric_OR_missing-method}
 \title{Flexibly bin paired ranges}
 \usage{
-assignToBins(x, binSize, pos1 = "center", pos2 = "center", ...)
+binPairs(x, binSize, pos1 = "center", pos2 = "center", ...)
 
-\S4method{assignToBins}{DF_OR_df_OR_dt,numeric,character_OR_numeric_OR_missing,character_OR_numeric_OR_missing}(x, binSize, pos1, pos2)
+\S4method{binPairs}{DF_OR_df_OR_dt,numeric,character_OR_numeric_OR_missing,character_OR_numeric_OR_missing}(x, binSize, pos1, pos2)
 
-\S4method{assignToBins}{GInteractions,numeric,character_OR_numeric_OR_missing,character_OR_numeric_OR_missing}(x, binSize, pos1, pos2)
+\S4method{binPairs}{GInteractions,numeric,character_OR_numeric_OR_missing,character_OR_numeric_OR_missing}(x, binSize, pos1, pos2)
 }
 \arguments{
 \item{x}{`GInteractions` or `data.frame`-like
@@ -48,7 +48,7 @@ df1 <-
                chr2 = "chr1", y1 = 30000, y2 = 40000)
 
 ## Assign each range to 20-kb bins from the start positions
-assignToBins(x = df1,
+binPairs(x = df1,
          binSize = 20000,
          pos1 = 'start',
          pos2 = 'start')
@@ -61,7 +61,7 @@ gi1 <-
     as_ginteractions()
 
 ## Assign each range to 20-kb bins from the start positions
-assignToBins(x = gi1,
+binPairs(x = gi1,
          binSize = 20000,
          pos1 = 'start',
          pos2 = 'start')
diff --git a/man/calcLoopEnrichment.Rd b/man/calcLoopEnrichment.Rd
index 4c86136..fb4a031 100644
--- a/man/calcLoopEnrichment.Rd
+++ b/man/calcLoopEnrichment.Rd
@@ -111,7 +111,7 @@ loops <-
 GenomeInfoDb::seqlevelsStyle(loops) <- 'ENSEMBL'
 
 ## Expand binSize of loops
-loops <- assignToBins(x=loops, binSize=100e3)
+loops <- binPairs(x=loops, binSize=100e3)
 
 ## Calculate loop enrichment
 calcLoopEnrichment(x=loops[1:10],
@@ -131,7 +131,7 @@ calcLoopEnrichment(x=loops[1:10],
                    bg=bg)
 
 ## Extract count matrices first
-mats <- assignToBins(loops[1:10],100e3) |>
+mats <- binPairs(loops[1:10],100e3) |>
   pixelsToMatrices(buffer=10) |>
     pullHicMatrices(
     files=hicFiles,
diff --git a/man/changePixelRes.Rd b/man/changePixelRes.Rd
index 1e5e134..7760493 100644
--- a/man/changePixelRes.Rd
+++ b/man/changePixelRes.Rd
@@ -124,7 +124,7 @@ loops <-
 GenomeInfoDb::seqlevelsStyle(loops) <- 'ENSEMBL'
 
 ## Rebin loops to 2.5e6 resolution
-loops <- assignToBins(x=loops, binSize=2.5e06)
+loops <- binPairs(x=loops, binSize=2.5e06)
 
 ## Change pixel resolution from 2.5e6 to 500e3
 changePixelRes(x=loops[1:5],
diff --git a/man/clusters.Rd b/man/getPairClusters.Rd
similarity index 79%
rename from man/clusters.Rd
rename to man/getPairClusters.Rd
index 468f9ee..aeaa83c 100644
--- a/man/clusters.Rd
+++ b/man/getPairClusters.Rd
@@ -1,13 +1,13 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/AllGenerics.R, R/methods-MergedGInteractions.R
-\name{clusters}
-\alias{clusters}
-\alias{clusters,MergedGInteractions-method}
+\name{getPairClusters}
+\alias{getPairClusters}
+\alias{getPairClusters,MergedGInteractions-method}
 \title{Get clustered pairs from MergedGInteractions object}
 \usage{
-clusters(x, ...)
+getPairClusters(x, ...)
 
-\S4method{clusters}{MergedGInteractions}(x)
+\S4method{getPairClusters}{MergedGInteractions}(x)
 }
 \arguments{
 \item{x}{MergedGInteractions object.}
@@ -50,10 +50,10 @@ x <- mergePairs(x = giList,
                 radius = 10e03,
                 column = "APScoreAvg")
 
-## Access pair clusters
-clusters(x[1:3])
-clusters(x[3:1])
-clusters(x[c(3, 1, 2)])
-clusters(x) |> length()
+## Access pair getPairClusters
+getPairClusters(x[1:3])
+getPairClusters(x[3:1])
+getPairClusters(x[c(3, 1, 2)])
+getPairClusters(x) |> length()
 
 }
diff --git a/man/pileupPixels.Rd b/man/pileupPixels.Rd
index 6c4abd1..87e28b1 100644
--- a/man/pileupPixels.Rd
+++ b/man/pileupPixels.Rd
@@ -106,7 +106,7 @@ loops <-
     setNames("WT") |>
     read.table(header=TRUE, nrows=1000) |>
     as_ginteractions(keep.extra.columns=FALSE) |>
-    assignToBins(binSize=5e3)
+    binPairs(binSize=5e3)
 
 ## Removes the "chr" prefix for compatibility
 ## with the preprocessed hic files
diff --git a/man/pullHicMatrices.Rd b/man/pullHicMatrices.Rd
index 1ff7f08..648313b 100644
--- a/man/pullHicMatrices.Rd
+++ b/man/pullHicMatrices.Rd
@@ -130,7 +130,7 @@ pixels <-
   setNames("WT") |>
   read.table(header=TRUE) |>
   as_ginteractions(keep.extra.columns=FALSE) |>
-  assignToBins(binSize=100e3)
+  binPairs(binSize=100e3)
 
 ## Removes the "chr" prefix for compatibility
 ## with the preprocessed hic files
diff --git a/man/pullHicPixels.Rd b/man/pullHicPixels.Rd
index 56a0836..76b7eff 100644
--- a/man/pullHicPixels.Rd
+++ b/man/pullHicPixels.Rd
@@ -120,7 +120,7 @@ pixels <-
   setNames("WT") |>
   read.table(header=TRUE) |>
   as_ginteractions(keep.extra.columns=FALSE) |>
-  assignToBins(binSize=100e3)
+  binPairs(binSize=100e3)
 
 ## Removes the "chr" prefix for compatibility
 ## with the preprocessed hic files
diff --git a/man/selectPixel.Rd b/man/selectPixel.Rd
index 194ce38..29fd512 100644
--- a/man/selectPixel.Rd
+++ b/man/selectPixel.Rd
@@ -75,7 +75,7 @@ loops <-
 GenomeInfoDb::seqlevelsStyle(loops) <- 'ENSEMBL'
 
 ## Rebin loops to 2.5e6 resolution
-loops <- assignToBins(x=loops, binSize=2.5e06)
+loops <- binPairs(x=loops, binSize=2.5e06)
 
 ## Pull 5x5 matrices
 iarr <- pullHicMatrices(x=loops[1:5],
diff --git a/man/sets.Rd b/man/subsetBySource.Rd
similarity index 70%
rename from man/sets.Rd
rename to man/subsetBySource.Rd
index 5190ca7..75eea1a 100644
--- a/man/sets.Rd
+++ b/man/subsetBySource.Rd
@@ -1,22 +1,22 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/AllGenerics.R, R/methods-MergedGInteractions.R
-\name{sets}
-\alias{sets}
-\alias{sets,MergedGInteractions,missing,missing-method}
-\alias{sets,MergedGInteractions,character_OR_missing,missing-method}
-\alias{sets,MergedGInteractions,missing,character_OR_missing-method}
-\alias{sets,MergedGInteractions,character_OR_missing,character_OR_missing-method}
+\name{subsetBySource}
+\alias{subsetBySource}
+\alias{subsetBySource,MergedGInteractions,missing,missing-method}
+\alias{subsetBySource,MergedGInteractions,character_OR_missing,missing-method}
+\alias{subsetBySource,MergedGInteractions,missing,character_OR_missing-method}
+\alias{subsetBySource,MergedGInteractions,character_OR_missing,character_OR_missing-method}
 \title{Get each set from a MergedGInteractions object}
 \usage{
-sets(x, include, exclude)
+subsetBySource(x, include, exclude)
 
-\S4method{sets}{MergedGInteractions,missing,missing}(x)
+\S4method{subsetBySource}{MergedGInteractions,missing,missing}(x)
 
-\S4method{sets}{MergedGInteractions,character_OR_missing,missing}(x, include)
+\S4method{subsetBySource}{MergedGInteractions,character_OR_missing,missing}(x, include)
 
-\S4method{sets}{MergedGInteractions,missing,character_OR_missing}(x, exclude)
+\S4method{subsetBySource}{MergedGInteractions,missing,character_OR_missing}(x, exclude)
 
-\S4method{sets}{MergedGInteractions,character_OR_missing,character_OR_missing}(x, include, exclude)
+\S4method{subsetBySource}{MergedGInteractions,character_OR_missing,character_OR_missing}(x, include, exclude)
 }
 \arguments{
 \item{x}{MergedGInteractions object.}
@@ -44,8 +44,8 @@ merged pair is not returned.
 }
 \details{
 Optional `include` and `exclude` parameters modulate
-the behavior of `sets` to return different
-subsets of originating pairs. For example, `include` requires
+the behavior of `subsetBySource` to return different
+subsubsetBySource of originating pairs. For example, `include` requires
 that the returned pairs be present in specific sources,
 while `exclude` requires that returned pairs be absent
 from specific sources. Sources not listed in either
@@ -78,6 +78,6 @@ giList <- split(x = GInteractions(gr1, gr2),
 ## Merge pairs
 x <- mergePairs(x = giList, radius = 20)
 
-sets(x)
+subsetBySource(x)
 
 }
diff --git a/tests/testthat/Rplots.pdf b/tests/testthat/Rplots.pdf
new file mode 100644
index 0000000..7a5f8a8
Binary files /dev/null and b/tests/testthat/Rplots.pdf differ
diff --git a/tests/testthat/_snaps/MergedGInteractions.md b/tests/testthat/_snaps/MergedGInteractions.md
index f27c0ed..07b5b12 100644
--- a/tests/testthat/_snaps/MergedGInteractions.md
+++ b/tests/testthat/_snaps/MergedGInteractions.md
@@ -24,12 +24,12 @@
          Avg_diffMaxNeihgboor_1 Avg_diffMaxNeihgboor_2      avg       std    value
       1:              1.8755854               2.121637 2.605124 0.7942202 4.272311
       2:              1.8755854               2.121637 2.605124 0.7942202 4.272311
-      3:              1.9105295               1.946362 1.854944 0.6729783 3.553193
-      4:              1.9105295               1.946362 1.854944 0.6729783 3.553193
+      3:              1.9105295               1.946361 1.854944 0.6729783 3.553193
+      4:              1.9105295               1.946361 1.854944 0.6729783 3.553193
       5:              1.0059373               1.645508 3.437883 0.5164226 4.332049
       6:              1.0059373               1.645508 3.437883 0.5164226 4.332049
-      7:              0.8104557               1.486894 3.200528 0.6733462 3.920933
-      8:              0.8104557               1.486894 3.200528 0.6733462 3.920933
+      7:              0.8104557               1.486893 3.200528 0.6733462 3.920933
+      8:              0.8104557               1.486893 3.200528 0.6733462 3.920933
          src id grp clst i.id
       1:  FS  1   1    1    1
       2:  FS  5   1    1    1
diff --git a/tests/testthat/_snaps/regularize.md b/tests/testthat/_snaps/regularize.md
index 3575f29..9cee0bb 100644
--- a/tests/testthat/_snaps/regularize.md
+++ b/tests/testthat/_snaps/regularize.md
@@ -2,7 +2,7 @@
 
     Code
       counts(regularize(ija, ndim = c(3, 3), scale = FALSE))
-    Message <simpleMessage>
+    Message
       / Reading and realizing block 1/3 of file 1/1 ... 
       OK
       \ Processing it ... 
diff --git a/tests/testthat/test_InteractionJaggedArray.R b/tests/testthat/test_InteractionJaggedArray.R
index 60796c6..e6373ab 100644
--- a/tests/testthat/test_InteractionJaggedArray.R
+++ b/tests/testthat/test_InteractionJaggedArray.R
@@ -107,7 +107,7 @@ test_that("InteractionJaggedArray subsetByOverlaps", {
 
 
     ## Shift first two ranges out of range
-    gi2 <- c(assignToBins(gi[1:2], binSize=100e3, pos1=-200e3), gi[3:4])
+    gi2 <- c(binPairs(gi[1:2], binSize=100e3, pos1=-200e3), gi[3:4])
 
     ## findOverlaps
     expect_identical(length(findOverlaps(iarr, iarr)), 4L)
diff --git a/tests/testthat/test_MergedGInteractions.R b/tests/testthat/test_MergedGInteractions.R
index f34b62f..c515535 100644
--- a/tests/testthat/test_MergedGInteractions.R
+++ b/tests/testthat/test_MergedGInteractions.R
@@ -61,29 +61,29 @@ test_that(".mapIds returns expected output", {
     expect_snapshot(x = .mapIds(x))
 })
 
-test_that("clusters accessor works", {
+test_that("getPairClusters accessor works", {
 
     ## Merge pairs and add names
     x <- mergePairs(x = giList, radius = 10e03)
     names(x) <- paste0("loop", 1:length(x))
 
     x[3:1] |>
-        clusters() |>
+        getPairClusters() |>
         names() |>
         expect_identical(paste0("loop", 3:1))
 
     x[1:3] |>
-        clusters() |>
+        getPairClusters() |>
         names() |>
         expect_identical(paste0("loop", 1:3))
 
-    expect_equal(length(clusters(x)), length(x))
+    expect_equal(length(getPairClusters(x)), length(x))
 
 })
 
-## TODO: Modfiy sets to return all sets
+## TODO: Modfiy subsetBySource to return all subsetBySource
 ## by default
-test_that("sets method works (and sources accessor)", {
+test_that("subsetBySource method works (and sources accessor)", {
 
     ## LIMA loops test
     loopFiles <- c(
@@ -114,71 +114,71 @@ test_that("sets method works (and sources accessor)", {
     ## Test sources accessor
     expect_identical(sources(x), names(loopFiles))
 
-    ## sets method dispatch
-    expect_equal(sets(x) |> length(), 255)
-    expect_equal(sets(x)[[sources(x)[1]]] |> length(), 846)
-    expect_equal(sets(x, include = sources(x)[1]) |> length(), 3982)
-    expect_equal(sets(x, exclude = sources(x)[1]) |> length(), 9890)
+    ## subsetBySource method dispatch
+    expect_equal(subsetBySource(x) |> length(), 255)
+    expect_equal(subsetBySource(x)[[sources(x)[1]]] |> length(), 846)
+    expect_equal(subsetBySource(x, include = sources(x)[1]) |> length(), 3982)
+    expect_equal(subsetBySource(x, exclude = sources(x)[1]) |> length(), 9890)
 
     ## Handles cases where none are found
-    sets(x,
+    subsetBySource(x,
            include = sources(x)[1],
            exclude = sources(x)[1]) |>
         length() |>
         expect_equal(0)
-    sets(x,
+    subsetBySource(x,
            include = sources(x)[1:2],
            exclude = sources(x)[1]) |>
         length() |>
         expect_equal(0)
-    sets(x, exclude = sources(x)) |>
+    subsetBySource(x, exclude = sources(x)) |>
         length() |>
         expect_equal(0)
 
     ## Handles improper source name
-    expect_error(sets(x, include = "foo"),
+    expect_error(subsetBySource(x, include = "foo"),
                  ".*foo.*not source option")
-    expect_error(sets(x, exclude = "foo"),
+    expect_error(subsetBySource(x, exclude = "foo"),
                  ".*foo.*not source option")
-    expect_error(sets(x, include = ""),
+    expect_error(subsetBySource(x, include = ""),
                  ".*not source option")
-    expect_error(sets(x, exclude = ""),
+    expect_error(subsetBySource(x, exclude = ""),
                  ".*not source option")
-    expect_error(sets(x, include = "foo", exclude = "foo"),
+    expect_error(subsetBySource(x, include = "foo", exclude = "foo"),
                  ".*foo.*not source option")
-    expect_error(sets(x, include = "foo", exclude = "bar"),
+    expect_error(subsetBySource(x, include = "foo", exclude = "bar"),
                  ".*foo.*bar.*not source option")
-    expect_error(sets(x,
+    expect_error(subsetBySource(x,
                         include = c(sources(x)[1], "foo"),
                         exclude = "bar"),
                  ".*foo.*bar.*not source option")
 
-    ## sets(x) produces same result as
+    ## subsetBySource(x) produces same result as
     ## using include & exclude
-    expect_equal(length(sets(x)[[sources(x)[1]]]),
-                 length(sets(x,
+    expect_equal(length(subsetBySource(x)[[sources(x)[1]]]),
+                 length(subsetBySource(x,
                                include = sources(x)[1],
                                exclude = sources(x)[2:8])))
 
-    ## sets(x) produces same result as
+    ## subsetBySource(x) produces same result as
     ## include/exclude for the first 8 sources
     expect_equal(
         lapply(seq_along(sources(x)), \(i){
             j <- seq_along(sources(x))[-i]
-            sets(x = x,
+            subsetBySource(x = x,
                            include = sources(x)[i],
                            exclude = sources(x)[j])
         }) |>
             lapply(length) |>
             unlist(),
-        sets(x)[1:8] |> lapply(length) |> unlist() |> unname()
+        subsetBySource(x)[1:8] |> lapply(length) |> unlist() |> unname()
     )
     
-    ## Results track with clusters(x)
-    mgi <- sets(x,
+    ## Results track with getPairClusters(x)
+    mgi <- subsetBySource(x,
                           include = sources(x)[1:2],
                           exclude = sources(x)[3:8])
-    expect_identical(clusters(mgi) |>
+    expect_identical(getPairClusters(mgi) |>
                          lapply(`[[`, "src") |>
                          unlist() |>
                          unique() |>
@@ -210,7 +210,7 @@ test_that("Aggregating metadata columns works", {
     expect_identical(object = aggMetadata(x[1:10],
                                            columns = "APScoreAvg",
                                            funs = "mean")$mean.APScoreAvg,
-                     expected = clusters(x[1:10]) |>
+                     expected = getPairClusters(x[1:10]) |>
                          lapply(`[[`, "APScoreAvg") |>
                          lapply(mean) |>
                          unlist())
diff --git a/tests/testthat/test_adjustEnrichment.R b/tests/testthat/test_adjustEnrichment.R
index 8217ddf..5c39007 100644
--- a/tests/testthat/test_adjustEnrichment.R
+++ b/tests/testthat/test_adjustEnrichment.R
@@ -22,7 +22,7 @@ GenomeInfoDb::seqlevelsStyle(loops) <- 'ENSEMBL'
 
 ## Calculate loop enrichment
 enrich <- calcLoopEnrichment(
-    x=assignToBins(loops, 100e03),
+    x=binPairs(loops, 100e03),
     files=hicFiles
 )
 
diff --git a/tests/testthat/test_aggHicMatrices.R b/tests/testthat/test_aggHicMatrices.R
index 1613d83..6d6657b 100644
--- a/tests/testthat/test_aggHicMatrices.R
+++ b/tests/testthat/test_aggHicMatrices.R
@@ -23,7 +23,7 @@ GenomeInfoDb::seqlevelsStyle(loops) <- 'ENSEMBL'
 
 ## Expand pixel ranges with a 5 pixel buffer on either side
 loops <-
-    assignToBins(loops, binSize=100e3) |>
+    binPairs(loops, binSize=100e3) |>
     pixelsToMatrices(buffer=5)
 
 ## Extract 10, 11x11 count matrices from 2 hic files
diff --git a/tests/testthat/test_binPairs.R b/tests/testthat/test_binPairs.R
index bc0982f..b7387c4 100644
--- a/tests/testthat/test_binPairs.R
+++ b/tests/testthat/test_binPairs.R
@@ -12,7 +12,7 @@ gi1 <-
 
 ## Tests -----------------------------------------------------------------------
 
-test_that("assignToBins can expand the resolution (from start)", {
+test_that("binPairs can expand the resolution (from start)", {
 
     ## Construct GInteractions from data.frame
     exp <-
@@ -21,7 +21,7 @@ test_that("assignToBins can expand the resolution (from start)", {
         as_ginteractions()
 
     obj <-
-        assignToBins(x = gi1,
+        binPairs(x = gi1,
                  binSize = 20000,
                  pos1 = 'start',
                  pos2 = 'start')
@@ -45,7 +45,7 @@ test_that("Bin to the TSS of one anchor", {
         as_ginteractions()
 
     obj <-
-        assignToBins(x = gi2,
+        binPairs(x = gi2,
                  binSize = 1000,
                  pos1 = 'start',
                  pos2 = 2000)
@@ -54,7 +54,7 @@ test_that("Bin to the TSS of one anchor", {
 
 })
 
-test_that("assignToBins retains metadata", {
+test_that("binPairs retains metadata", {
 
     ## Construct GInteractions from data.frame
     exp <-
@@ -67,7 +67,7 @@ test_that("assignToBins retains metadata", {
     gi1$var2 <- 10
 
     obj <-
-        assignToBins(x = gi1,
+        binPairs(x = gi1,
                  binSize = 20000,
                  pos1 = 'start',
                  pos2 = 'start')
@@ -76,7 +76,7 @@ test_that("assignToBins retains metadata", {
 
 })
 
-test_that("assignToBins doesn't modify class", {
+test_that("binPairs doesn't modify class", {
 
     ## Load required packages
     library(data.table)
@@ -102,7 +102,7 @@ test_that("assignToBins doesn't modify class", {
 
     ## Binning
     bmgi <-
-        assignToBins(x = mgi,
+        binPairs(x = mgi,
                  binSize = 10e03,
                  pos1 = 'start',
                  pos2 = 'end')
@@ -113,7 +113,7 @@ test_that("assignToBins doesn't modify class", {
 
     ## For non merged data
     bp <-
-        assignToBins(x = giList[[1]],
+        binPairs(x = giList[[1]],
                  binSize = 10e03,
                  pos1 = 'start',
                  pos2 = 'end')
@@ -124,12 +124,12 @@ test_that("assignToBins doesn't modify class", {
 })
 
 test_that("Binning checks for appropriate binSize", {
-    assignToBins(gi1, binSize = 0) |>
+    binPairs(gi1, binSize = 0) |>
         expect_error("`binSize` must be > 0")
 })
 
 test_that("Anchors can be binned independently", {
-    bgi <- assignToBins(gi1, binSize=c(5e03, 1e03))
+    bgi <- binPairs(gi1, binSize=c(5e03, 1e03))
     expect_equal(unique(width(regions(bgi)))-1,
                  c(5e03, 1e03))
 })
diff --git a/tests/testthat/test_calcLoopEnrichment.R b/tests/testthat/test_calcLoopEnrichment.R
index 88deb86..bf9b12c 100644
--- a/tests/testthat/test_calcLoopEnrichment.R
+++ b/tests/testthat/test_calcLoopEnrichment.R
@@ -529,7 +529,7 @@ test_that("calcLoopEnrichment", {
 
     ## Doesn't accept loops of variable resolution
     loops |>
-        assignToBins(c(5e03, 10e03)) |>
+        binPairs(c(5e03, 10e03)) |>
         calcLoopEnrichment(files=hicFiles) |>
         expect_error("All ranges.*must be equal widths.")
 
@@ -556,7 +556,7 @@ test_that("calcLoopEnrichment", {
                    dim = c(10L, 2L),
                    dimnames = list(NULL, c("FS","WT"))
                ))
-    res <- calcLoopEnrichment(x=loops[1:10] |> assignToBins(100e03),
+    res <- calcLoopEnrichment(x=loops[1:10] |> binPairs(100e03),
                               files=hicFiles)
     expect_equal(res, exp)
     expect_s4_class(res, "DelayedMatrix")
@@ -585,7 +585,7 @@ test_that("InteractionArray method for calcLoopEnrichment runs correctly",{
  
    ## Test non-square matrices 
   mats <- 
-    assignToBins(loops[1:100],binSize = c(100e3, 50e3)) |>
+    binPairs(loops[1:100],binSize = c(100e3, 50e3)) |>
     pullHicMatrices(
       files=hicFiles,
       binSize=10e3,
@@ -597,7 +597,7 @@ test_that("InteractionArray method for calcLoopEnrichment runs correctly",{
   
   ## Test even matrices
   mats <- 
-    assignToBins(loops[1:100],binSize = 100e3) |>
+    binPairs(loops[1:100],binSize = 100e3) |>
     pullHicMatrices(
       files=hicFiles,
       binSize=50e3,
@@ -609,7 +609,7 @@ test_that("InteractionArray method for calcLoopEnrichment runs correctly",{
   
   ## Test non-matching buffers
   mats <- 
-    assignToBins(loops[1:100],100e3) |>
+    binPairs(loops[1:100],100e3) |>
     pixelsToMatrices(buffer=5) |>
     pullHicMatrices(
       files=hicFiles,
@@ -624,7 +624,7 @@ test_that("InteractionArray method for calcLoopEnrichment runs correctly",{
   ) |> expect_error("`buffer` must be the same")
   
   mats <- 
-    assignToBins(loops[1:100],100e3) |>
+    binPairs(loops[1:100],100e3) |>
     pixelsToMatrices(buffer=10) |>
     pullHicMatrices(
       files=hicFiles,
@@ -676,7 +676,7 @@ test_that("InteractionArray method for calcLoopEnrichment runs correctly",{
              ))
   
   mats <- 
-    assignToBins(loops[1:10],100e3) |>
+    binPairs(loops[1:10],100e3) |>
     pixelsToMatrices(buffer=5) |>
     pullHicMatrices(
       files=hicFiles,
@@ -731,7 +731,7 @@ test_that("calcLoopEnrichment function can use local environment objects",{
   expect_error(.modifyEnrichFun(simpleFun), "object.*not found")
   
   mats <- 
-    assignToBins(loops[1:10],100e3) |>
+    binPairs(loops[1:10],100e3) |>
     pixelsToMatrices(buffer=5) |>
     pullHicMatrices(
       files=hicFiles,
diff --git a/tests/testthat/test_changePixelRes.R b/tests/testthat/test_changePixelRes.R
index 548cdf2..872702d 100644
--- a/tests/testthat/test_changePixelRes.R
+++ b/tests/testthat/test_changePixelRes.R
@@ -20,7 +20,7 @@ loops <-
 GenomeInfoDb::seqlevelsStyle(loops) <- 'ENSEMBL'
 
 ## Rebin loops to 2.5e6 resolution
-loops <- assignToBins(x=loops, binSize=2.5e06)
+loops <- binPairs(x=loops, binSize=2.5e06)
 
 test_that("selectPixel chooses correctly", {
 
diff --git a/tests/testthat/test_mergePairs.R b/tests/testthat/test_mergePairs.R
index d610390..2bc6f90 100644
--- a/tests/testthat/test_mergePairs.R
+++ b/tests/testthat/test_mergePairs.R
@@ -345,8 +345,8 @@ test_that("Mean of modes option doesn't alter original ranges", {
     mgi1 <- mergePairs(x=gi, radius=binSize*2, column='count')
     mgi2 <- mergePairs(x=gi, radius=binSize*2)
     expect_identical(
-        clusters(mgi1),
-        clusters(mgi2)
+        getPairClusters(mgi1),
+        getPairClusters(mgi2)
     )
 
 })
diff --git a/tests/testthat/test_pileupPixels.R b/tests/testthat/test_pileupPixels.R
index 359c6dc..7e0832a 100644
--- a/tests/testthat/test_pileupPixels.R
+++ b/tests/testthat/test_pileupPixels.R
@@ -13,7 +13,7 @@ test_that("pileupPixels works", {
         setNames("WT") |>
         read.table(header=TRUE, nrows=1000) |>
         as_ginteractions(keep.extra.columns=FALSE) |>
-        assignToBins(binSize=5e3)
+        binPairs(binSize=5e3)
 
     ## Removes the "chr" prefix for compatibility
     ## with the preprocessed hic files
diff --git a/tests/testthat/test_pixelsToMatrices.R b/tests/testthat/test_pixelsToMatrices.R
index bf12209..b65e395 100644
--- a/tests/testthat/test_pixelsToMatrices.R
+++ b/tests/testthat/test_pixelsToMatrices.R
@@ -24,7 +24,7 @@ test_that("metadata columns are kept", {
 })
 
 test_that("throws error when ranges are not binned", {
-    assignToBins(gi, binSize=c(10, 20)) |>
+    binPairs(gi, binSize=c(10, 20)) |>
         pixelsToMatrices(buffer=3) |>
         expect_error(".*must be equal widths.*")
 })
diff --git a/tests/testthat/test_pullHic.R b/tests/testthat/test_pullHic.R
index 6d70048..ab75e1a 100644
--- a/tests/testthat/test_pullHic.R
+++ b/tests/testthat/test_pullHic.R
@@ -49,7 +49,7 @@ mgi <- mergePairs(x = giList,
                   radius = 50e03)
 
 ## Bin MergedGInteractions
-bgi <- assignToBins(x = mgi, binSize = 50e03)
+bgi <- binPairs(x = mgi, binSize = 50e03)
 
 ## Bin with snapping
 sgi <- snapToBins(x = mgi, binSize = 50e03)
@@ -237,7 +237,7 @@ test_that("Straw args are checked correctly", {
 test_that("pullHicPixels pulls correct counts", {
 
     ## Assign to x (to avoid modifying in place)
-    x <- assignToBins(bgi[1:10], 2.5e06)
+    x <- binPairs(bgi[1:10], 2.5e06)
     seqlevelsStyle(x) <- "ENSEMBL"
 
     ## Give names to hicFiles
diff --git a/tests/testthat/test_removeShortPairs.R b/tests/testthat/test_removeShortPairs.R
index 7996bda..bb995a4 100644
--- a/tests/testthat/test_removeShortPairs.R
+++ b/tests/testthat/test_removeShortPairs.R
@@ -80,7 +80,7 @@ test_that("complex test for removeShortPairs", {
     loops <-
         mergePairs(loopList, radius=100e3) |>
         GenomeInfoDb::`seqlevelsStyle<-`('ENSEMBL') |>
-        assignToBins(binSize=100e3)
+        binPairs(binSize=100e3)
 
     ## Expand to apa regions
     regions <- pixelsToMatrices(loops, buffer=5)
diff --git a/tests/testthat/test_utils.R b/tests/testthat/test_utils.R
index a5e06ea..adfcc72 100644
--- a/tests/testthat/test_utils.R
+++ b/tests/testthat/test_utils.R
@@ -177,7 +177,7 @@ test_that("Getting binSize", {
     .getBinSize(x=loops) |>
         expect_identical(5000)
 
-    .getBinSize(x=assignToBins(loops, 10e03)) |>
+    .getBinSize(x=binPairs(loops, 10e03)) |>
         expect_identical(10000)
 
 })
@@ -212,7 +212,7 @@ test_that("defaultBuffer returns correct result", {
   
   ## Extract count matrices
   mats <- 
-    assignToBins(loops[1:10],100e3) |>
+    binPairs(loops[1:10],100e3) |>
     pixelsToMatrices(buffer=testBuffer) |>
     pullHicMatrices(
       files=hicFiles,
diff --git a/vignettes/articles/pull_hic.Rmd b/vignettes/articles/pull_hic.Rmd
index a8947bd..01d3d89 100644
--- a/vignettes/articles/pull_hic.Rmd
+++ b/vignettes/articles/pull_hic.Rmd
@@ -49,7 +49,7 @@ border-bottom: 1px solid #dee2e6;
 </div>
 You can check your `.hic` file to see which resolutions
 are available for the `binSize` argument with the 
-`strawr::readHicBpResolutions()`. See the `assignToBins()`
+`strawr::readHicBpResolutions()`. See the `binPairs()`
 to set your interactions to an acceptable resolution.
 </div>
 
@@ -153,7 +153,7 @@ the width of both anchors to be 500 Kb
 
 ```{r}
 ## Create 500x500 Kb regions
-regions <- assignToBins(x=gi, binSize=500e3, pos1="start", pos2="start")
+regions <- binPairs(x=gi, binSize=500e3, pos1="start", pos2="start")
 ```
 
 Then set the `binSize` to 100 Kb
@@ -222,7 +222,7 @@ to be 600 Kb.
 
 ```{r}
 ## Create 300x600 Kb regions
-regions <- assignToBins(
+regions <- binPairs(
     x=gi,
     binSize=c(300e3, 600e3),
     pos1="start",
diff --git a/vignettes/mariner.Rmd b/vignettes/mariner.Rmd
index ecb7c32..34a470c 100644
--- a/vignettes/mariner.Rmd
+++ b/vignettes/mariner.Rmd
@@ -117,7 +117,7 @@ to differently sized bins.
 
 ```{r binning1, message=FALSE}
 ## Assign to 1Kb bins
-binned <- assignToBins(x=gi, binSize = 1e3, pos1='center', pos2='center')
+binned <- binPairs(x=gi, binSize = 1e3, pos1='center', pos2='center')
 
 ## Show that each anchor is 1Kb
 library(InteractionSet)
@@ -150,14 +150,14 @@ binned separately and from different reference points
 
 ```{r binning2}
 ## Assign anchor1 to 1Kb bins and anchor2 to 25Kb bins
-binned <- assignToBins(x=gi, binSize=c(1e3, 25e3), pos1="start", pos2="center")
+binned <- binPairs(x=gi, binSize=c(1e3, 25e3), pos1="start", pos2="center")
 
 ## Show that the first anchor is 1Kb and
 ## second anchor is 25Kb
 width(binned) |> lapply(unique)
 ```
 
-While `assignToBins()` assigns each pair of ranges
+While `binPairs()` assigns each pair of ranges
 to a single bin, the `snapToBins()` function 
 assigns the starts and ends of the ranges to
 their nearest bin. This allows each anchor to
@@ -256,7 +256,7 @@ The metadata is missing from these interactions.
 Since no `column` was provided, each interaction
 may be an average of one or more interaction.
 The user can decide how metadata from each cluster
-should be aggregated with `aggMetadata()`.
+should be aggregated with `aggPairMcols()`.
 </div>
 
 The resulting object is `MergedGInteractions` class,
@@ -266,11 +266,11 @@ behaves like `GInteractions` but contains additional
 information about the clustered interactions.
 
 To view the clusters of specific interactions, use
-the `clusters()` accessor.
+the `getPairClusters()` accessor.
 
 ```{r clusters, results='hold'}
 mgi[12772]
-clusters(mgi[12772])
+getPairClusters(mgi[12772])
 ```
 
 When no `column` argument is provided the most
@@ -297,10 +297,10 @@ for "APScoreAvg" has been selected.
 
 ```{r clusters2, results='hold'}
 mgi[12772]
-clusters(mgi[12772])
+getPairClusters(mgi[12772])
 ```
 
-The `sets()` accessor allows users to
+The `subsetBySource()` accessor allows users to
 find which interactions are shared or exclusive
 between sets of interactions in the giList.
 
@@ -309,15 +309,15 @@ between sets of interactions in the giList.
 sources(mgi)
 
 ## Interactions unique to each source
-sets(mgi) |> lapply(summary)
+subsetBySource(mgi) |> lapply(summary)
 
 ## Interactions shared by both sources
-sets(x=mgi, include=sources(mgi))
+subsetBySource(x=mgi, include=sources(mgi))
 ```
 
 This is particularly useful for identifying
 _de novo_, shared or transient interactions.
-For more information see `?sets()`.
+For more information see `?subsetBySource()`.
 
 ## Extracting & Aggregating Interactions
 
@@ -408,11 +408,11 @@ GenomeInfoDb::seqlevelsStyle(mgi) <- 'ENSEMBL'
 
 
 These interactions can then be binned to the desired
-resolution with the `assignToBins()` function.
+resolution with the `binPairs()` function.
 
 ```{r binPixels}
 ## Assign interactions to 100Kb bins
-binned <- assignToBins(x=mgi, binSize=100e3)
+binned <- binPairs(x=mgi, binSize=100e3)
 ```
 
 Contact frequency can then be extracted with
@@ -553,7 +553,7 @@ This also works on rectangular selections.
 ```{r pullMatrices3}
 
 ## Bin at two different resolutions
-binned <- assignToBins(x=mgi, binSize=c(100e3, 250e3))
+binned <- binPairs(x=mgi, binSize=c(100e3, 250e3))
 
 ## Pull 10x25 matrices from 1000 interactions and 2 hic files
 iarr2 <- pullHicMatrices(
@@ -682,7 +682,7 @@ loops <-
     setNames("WT") |>
     read.table(header=TRUE, nrows=1000) |>
     as_ginteractions() |>
-    assignToBins(binSize=100e3) |>
+    binPairs(binSize=100e3) |>
     GenomeInfoDb::`seqlevelsStyle<-`('ENSEMBL')
 
 ## Define foreground & background