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#' @param fold_changes Matrix specifying multiplicative fold changes |
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#' between groups. There is no default, so you must provide this argument. |
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#' In real data sets, lowly-expressed transcripts often show high fold |
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#' changes between groups, so this can be kept in mind when setting |
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#' \code{fold_changes} and \code{reads_per_transcript}. This argument must |
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#' have the same number of columns as there are groups as |
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#' specified by \code{num_reps}, and must have the same number of rows as |
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#' there are transcripts in \code{fasta}. A fold change of X in matrix entry |
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#' i,j means that for replicate j, the baseline mean number of reads |
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#' (reads_per_transcript[i]) will be multiplied by X. Note that the |
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#' multiplication happens before the negative binomial value |
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#' (for the number of reads that *actually will* be |
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#' drawn from transcript i, for replicate j) is drawn. This argument is |
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#' ignored if \code{length(num_reps)} is 1 (meaning you only have 1 group in |
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#' your simulation). |
A fold change of X in matrix entry i,j means that for replicate j, the baseline mean number of reads (reads_per_transcript[i]) will be multiplied by X.
should probably be
A fold change of X in matrix entry i,j means that for group j, the baseline mean number of reads (reads_per_transcript[i]) will be multiplied by X.
