bioinfo_rmd_contrasts: Write Bioinfo RMD

In jdreyf/bioinformd: Construct RMD analysis files

Write Bioinfo RMD

Description

Write Bioinformatics RMD workflow.

Usage

bioinfo_rmd_contrasts(
  filename,
  local.path = NULL,
  data.desc = "Gene expression",
  input.files,
  data.logged = TRUE,
  data.nas = TRUE,
  grp.var = "grp",
  covars = NULL,
  aw.model = paste0("~0+", grp.var),
  use_aw = TRUE,
  use_trend = FALSE,
  contr.v,
  limma.model = NULL,
  row.type = "gene",
  gmt_abbrev = c("reactome", "tft"),
  gmt_prefix = c("c2.cp.reactome", "c3.tft.gtrd")
)

Arguments

filename	Filename of RMD.
local.path	Path of RMD.
data.desc	Description of data sources for input.files.
input.files	Character vector of input files. Matrix, pheno, and (optionally) annot.
data.logged	Logical indicating if data has been log2-transformed.
data.nas	Logical indicating if data has NAs.
grp.var	Variable name in pheno for group.
covars	Variable name in pheno for covariates.
aw.model	Model for 'limma::arrayWeights'.
use_aw	Logical indicating if array weights should be used.
use_trend	Logical indicating if limma trend should be used.
contr.v	Named vector of contrasts.
limma.model	Model formula for limma, if want a design matrix.
row.type	Character in filename for features.
gmt_abbrev	Character vector of abbreviation of pathway name, e.g. "reactome" or "tft".
gmt_prefix	Character vector of GMT file(s) prefixes.

Details

If need to remove a sample, rerun with new input.files.

Examples

bioinfo_rmd_contrasts(filename="new_analysis", input.files = c("counts.csv", "pheno.csv"),
contr.v='c(treat="treat-control")')

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