limma_module: Limma module taking metadata_csv and raw count data frame to...

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

Description

Limma module taking metadata_csv and raw count data frame to run DE analysis

Usage

limma_module(
  count_data,
  anno_tb = NULL,
  tpm_tb = NULL,
  tag = NULL,
  metadata_csv = NULL,
  metadata_design = NULL,
  control_reference = NULL,
  output_dir = NULL,
  delim_samples = "\\.",
  run_voom = FALSE
)

Arguments

count_data	object in matrix format (integers) with rownames as genes and colnames as sample IDs
anno_tb	data frame of ensembl_gene_id - external_gene_id mappings for annotation
tpm_tb	data frame of tpms to append to results for output
tag	string used to prefix output
metadata_csv	path to file holding metadata
metadata_design	string of design using colnames of metadata_csv BN that final entry is the
control_reference	string indicating the 'control' intgroup for last element of design
output_dir	path to where output goes
delim_samples	character to delimit sample IDs (default: ".")

Value

nz_fc_co raw count object with no lines summing to zeros

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