update documentation to reflect changes done in mariner v1.2.0

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)
@@ -79,19 +79,19 @@ 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)
 exportMethods(dim)
 exportMethods(end1)
 exportMethods(end2)
 exportMethods(findOverlaps)
+exportMethods(getPairClusters)
 exportMethods(hdf5BlockApply)
 exportMethods(interactions)
 exportMethods(length)
@@ -131,14 +131,14 @@ exportMethods(selectTopRight)
 exportMethods(selectionMethod)
 exportMethods(seqnames1)
 exportMethods(seqnames2)
-exportMethods(sets)
 exportMethods(shiftRanges)
 exportMethods(show)
 exportMethods(snapToBins)
 exportMethods(sources)
 exportMethods(start1)
 exportMethods(start2)
 exportMethods(subsetByOverlaps)
+exportMethods(subsetBySource)
 import(data.table,
  except = c(between, shift, first, second, indices))
 import(methods)

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

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

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)

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)

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
 #'

R/methods-adjustEnrichment.R

@@ -122,7 +122,7 @@
 #'
 #' ## Calculate loop enrichment
 #' enrich <- calcLoopEnrichment(
-#'     x=assignToBins(loops, 100e03),
+#'     x=binPairs(loops, 100e03),
 #'     files=hicFiles
 #' )
 #'

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