deseq2_lrt: Apply DESeq2's DESeq, results, and lfcShrink to one or more...
In jdreyf/jdcbioinfo: Joslin Diabetes Center bioinformatics utilities

deseq2_lrt

R Documentation

Apply DESeq2's DESeq, results, and lfcShrink to one or more contrasts, and return a data.frame

Description

Apply DESeq2's DESeq, results,and lfcShrink to one or more contrasts, and return a data.frame

Usage

deseq2_lrt(
  dds,
  grp = NULL,
  reduced = design(dds)[, 1],
  prefix = "Group",
  add.means = !is.null(grp),
  cols = c("stat", "pvalue", "padj"),
  ncore = 1
)

Arguments

`dds`	DESeqDataSet object.
`grp`	Vector of sample groups. These must be valid variable names in R and the same length as `ncol(object)`.
`reduced`	model matrix of the reduced model
`prefix`	the prefix for the test result columns
`add.means`	Logical indicating if (unweighted) group means per row should be added to the output.
`cols`	Columns of `topTable` output to include. Possibilities include `"logFC", "SE", "AveExpr", "z", "t", "P.Value", "adj.P.Val", "CI.L", "CI.R", "B"`. Some of these column names are then changed here. If `logFC` is specified, `FC` will automatically also be given.
`ncore`	Number of cores to use.