gene_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, optionally makes boxplots of the comparison, faceted by gene used in a pipeline, so checks are pretty rudimentary

gene_compare(
  dat,
  geneSet,
  grp1name = "group1",
  grp2name = "group2",
  grp1idx,
  grp2idx,
  plot = FALSE
)

`dat`	A matrix of gene expression
`geneSet`	A vector of gene names in the gene expression matrix above
`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
`plot`	Boolean indicating whether to draw boxplots using ggplot2

table of genes' mean expression values for each group

## Not run: 
out <- gene_compare(expressionMatrix
                   ,c("LAP3","NCOA7","IFIT2","STAT1","TRIM21")
                   ,grp1name = "control"
                   ,grp2name = "experimental"
                   ,which(grepl("control", colnames(expressionMatrix)))
                   ,which(grepl("experimental", colnames(expressionMatrix)))
                                  )

## End(Not run)