diff_da: Difference analysis

In pctax: Professional Comprehensive Omics Data Analysis

Difference analysis

Description

Difference analysis

Usage

diff_da(
  otutab,
  group_df,
  ctrl = NULL,
  method = "deseq2",
  log = TRUE,
  add_mini = NULL,
  ...
)

Arguments

otutab	otutab
group_df	a dataframe with rowname same to dist and one group column
ctrl	the control group, one level of groups
method	one of "deseq2","edger","limma","t.test","wilcox.test"
log	do log transfer for limma?
add_mini	add_mini when calculate the logFC. e.g (10+0.1)/(0+0.1), default 0.5*min(abundance)
...	other parameters

Value

a dataframe

Examples

if (requireNamespace("limma")) {
  data(otutab, package = "pcutils")
  diff_da(otutab, metadata["Group"], method = "limma") -> res
  volcano_p(res)
  volcano_p(res, mode = 2)
}

pctax documentation built on May 29, 2024, 10:03 a.m.