DESeq_cov_asso: DESeq2 covariate associations with OTUs

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

Description

DESeq2 covariate associations with OTUs

Usage

DESeq_cov_asso(
  phyloseq_obj,
  day,
  tissue,
  covariate,
  shrink_type = "apeglm",
  cookscut = TRUE,
  treatment = FALSE,
  scale_cov = TRUE,
  p.plot = 0.05,
  plot_lab = "Genus",
  l2fc_plot = 0.25
)

Arguments

phyloseq_obj	A phyloseq object, must have tax table
day	Day to prune the phyloseq object to
tissue	tissue to prune the phyloseq object to
covariate	Covariate in sample data to calculate associations for, as a string.
shrink_type	DESeq2 shrink type
cookscut	Apply cooks cutoff?
treatment	include 'treatment' in formula?
scale_cov	scale the covariate?
p.plot	pvalue to filter plot by
plot_lab	taxonomic level to use for plotting
l2fc_plot	lfc2 to filter plot by

Value

returns a list of lenth 2, 1st is plot 2nd is data

Examples

#soon

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