roast_contrasts_chunk: Roast contrasts chunk

In jdreyf/bioinformd: Construct RMD analysis files

Roast contrasts chunk

Description

Roast contrasts chunk.

Usage

roast_contrasts_chunk(
  grp.var,
  path,
  gmt_abbrev = c("reactome", "gtrd", "mirdb"),
  gmt_prefix = c("c2.cp.reactome", "c3.tft.gtrd", "c3.mir.mirdb"),
  use_des = FALSE,
  use_aw = TRUE,
  use_trend = FALSE,
  elst = FALSE
)

Arguments

grp.var	Variable name in pheno for group.
path	Path of RMD.
gmt_abbrev	Character vector of abbreviation of pathway name, e.g. "reactome" or "tft".
gmt_prefix	Character vector of GMT file(s) prefixes.
use_des	Logical indicating if design (from limma chunk) should be used.
use_aw	Logical indicating if array weights should be used.
use_trend	Logical indicating if limma trend should be used.
elst	Logical indicating if expression object an EList.

jdreyf/bioinformd documentation built on June 14, 2025, 10:59 p.m.