deseq2_biom: Run DESeq2 on a phyloseq object and return tibble of...

In jhbadger/cipphyloseq: Adds Additional Features (plots, DESeq2) to phyloseq

Description

Run DESeq2 on a phyloseq object and return tibble of significantly abundant OTUs

Usage

deseq2_biom(biom, taxlevel, group, alpha = 0.01, threshold = 1,
  glom = TRUE, pseudocounts = 0, maxgroups = 5)

Arguments

biom	a phyloseq object.
taxlevel	string giving taxonomic level (from tax_table) to compare at.
group	string giving column in sample data to compare
alpha	p-value cutoff
threshold	minimum percentage of OTU to report
glom	run tax_glom on biom to get to desired level (FALSE if already at right level)

Examples

deseq2_biom()

jhbadger/cipphyloseq documentation built on May 24, 2019, 2:04 a.m.