deseq_contrasts: Perform DESeq using contrasts

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

Description

You could just call DESeq() in your code... or you could call this nifty function, which also saves the output to a table AND an R variable for later use

Usage

deseq_contrasts(dds, myAlpha, myContrast, nickname, currDate, expName,
  genesOfInterest)

Arguments

dds	DESeq object
myAlpha	number - threshold for calling genes significant
myContrast	c('Factor To Study in Contrast', 'Level1', 'Level2')
nickname	Character string - what do you want these results to be called
currDate	Character string - code representing date on which you did this analysis
expName	Character string - code representing this whole set of analyses
genesOfInterest	Dataframe column listing genes you might want to count in plot, e.g. sex marker genes

Details

Returns DESeq results object.

Examples

results_SexEffect_mainEffect <- deseq_contrasts(dds_sva, 0.05, c("Sex", "F", "M"), 'results_SexEffect_mainEffect', '20180814', 'exploreNewData', amySexGenes[,2])

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