run_prep_modules_bm: Wrap prep and module for data from brucemoran RNAseq_kallisto...

In brucemoran/RNAseqR: RNAseq DE Analysis Downstream from Nextflow Pipelines

Description

Wrap prep and module for data from brucemoran RNAseq_kallisto Nextflow pipeline

Usage

run_prep_modules_bm(
  metadata_csv,
  metadata_design,
  tag,
  output_dir = NULL,
  data_dir = NULL,
  control_reference = NULL,
  genome_prefix = "hsapiens",
  msigdb_species = "Homo sapiens",
  msigdb_cat = "H",
  server_threads = NULL
)

Arguments

metadata_csv	path to file holding metadata
metadata_design	string of design using colnames of metadata_csv
tag	string used to prefix output
output_dir	path to where output goes
data_dir	path to where data recurse search begins
control_reference	string indicating the 'control' intgroup for last element of design
genome_prefix	string of a genome in biomart$dataset, suffixed with '_gene_ensembl'
msigdb_species	one of msigdbr::msigdbr_show_species(), default:"Homo sapiens"
msigdb_cat	one of 'c("H", paste0("C", c(1:7)))', see: gsea-msigdb.org/gsea/msigdb/collections.jsp
server_threads	set to anything but NULL to allow threading

Value

none rds and tsv files printed

brucemoran/RNAseqR documentation built on Sept. 14, 2021, 11:08 a.m.