category_compare: compares the mean expression between two groups of genes in a...
In ptvan/Pmisc: Phu's Misc Functions

Description Usage Arguments Value Examples

compares the mean expression between two groups of genes in a given expression matrix, calculates the number and proportion of genes in the input matrix that are up-regulated

category_compare(
  dat,
  setsIndices,
  grp1name = "group1",
  grp2name = "group2",
  grp1idx,
  grp2idx
)

`dat`	A matrix of gene expression
`setsIndices`	A nested-list of gene indices for each GSEA category, most commonly made from limma::ids2indices()
`grp1name`	String indicating name of the first group for the comparison
`grp2name`	String indicating name of the second group for the comparison
`grp1idx`	A vector of integer indices indicating columns belonging to group1
`grp2idx`	A vector of integer indices indicating columns belonging to group1

table of genes' mean expression values for each group

## Not run: 
out <- category_compare(expressionMatrix,
                                  setIndices,
                                  grp1name = "control",
                                  grp2name = "experimental",
                                  which(grepl("control", colnames(expressionMatrix))),
                                  which(grepl("experimental", colnames(expressionMatrix)))
                                  )

## End(Not run)