deseq2_cor: Apply DESeq2's DESeq, results, and lfcShrink to one or more...

In jdreyf/jdcbioinfo: Joslin Diabetes Center bioinformatics utilities

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_cor(
  dds,
  name = colnames(design(dds))[2],
  cols = c("pvalue", "padj", "log2FoldChange"),
  ncore = 1,
  shrunken = TRUE
)

Arguments

dds	DESeqDataSet object.
name	Name of the individual effect (coefficient) to test
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.
shrunken	logical, whether to shrink the slope

jdreyf/jdcbioinfo documentation built on Feb. 12, 2025, 4:30 p.m.