Difference analysis — diff_da • pctax

Difference analysis

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

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