Arguments
counts
A matrix of counts where each row specifies a gene and each column specifies a replicate.
treatment
A vector specifying the treatment group for each column of the counts matrix. Only two treatment groups of either paired or unpaired data are allowed.
replic
A vector specifying the replicate for each column of the counts matrix when there is paired data; optional if data is unpaired.
sort.method
Character vector specifying one of "unpaired" or "paired", depending on the structure of the data.
sorted
logical vector specifying whether data has already gone through SortData function. Defaults to FALSE.
norm.factors
A positive numeric vector of multiplicative normalization factors for each column of the counts matrix.
exact
Specifies whether an exact signed rank test (paired) or exact ranksum test (unpaired) should be used.