DESeq_difabund: DESeq2 differential abundance for all treatments compared to...

In Jtrachsel/funfuns: Functions I Use (Title Case)

Description

DESeq2 differential abundance for all treatments compared to 'Control'

Usage

DESeq_difabund(
  phyloseq,
  day,
  tissue,
  scientific = TRUE,
  shrink_type = "normal",
  alpha = 0.1,
  cooks_cut = FALSE,
  pAdjustMethod = "BH"
)

Arguments

phyloseq	phyloseq object
day	day of interest (used to subset phyloseq object)
tissue	tissue of interest (used to subset phyloseq object)
scientific	change pvals to sci notation?
shrink_type	what type of lfc shrinkage? passed to DESeq2's lfc_shrink. should be one of 'normal', 'ashr', 'apeglm'.
alpha	passed to DESeq2 results() function.
cooks_cut	apply cooks cutoff?
pAdjustMethod	what type of p.adjustment to apply?

Value

returns a dataframe containing all the significantly differentially abundant taxa for each treatment in your experiment compared to the 'Controls'

Examples

#soon

Jtrachsel/funfuns documentation built on Aug. 8, 2021, 7:31 p.m.