pctax (version 0.1.3)

diff_da: Difference analysis

Description

Difference analysis

Usage

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

Value

a dataframe

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

Examples

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