add_lfcShrink: Add LFC Shrink

In kmuench/DESeqAid: DESeqAid: Kristin's favorite functions for her DESeq-based differential expression pipelines

Description

Takes in DESeq results object and turns it into a nice data frame, complete with column for shrunken lfcs.

Usage

add_lfcShrink(myResults, dds, myContrast)

Arguments

myResults	DESeq results object
dds	DESeq Object
myContrast	coefficient or contrast that you used to

Details

Returns data frame with DESeq results entries for each gene (significant and non-), with separate shrunken lfc column.

Generated in a rage when I got frustrated with trying to pass multiple objects in a list out of an R function. One day, this may get folded into deseq_coef or deseq_contrasts.

Examples

results_sex_df <- add_lfcShrink(results_sex, dds_sva, c('Sex', 'M', 'F'))

kmuench/DESeqAid documentation built on Oct. 14, 2020, 4:45 a.m.