deg_run: run DEG

In xiayh17/RNAseqStat: A Pipeline to Process RNAseq Data

run DEG

Description

run DEG module in limma, DESeq2 and edgeR

Usage

deg_run(
  counts_data,
  group_list,
  test_group = "T",
  control_group = "C",
  dir,
  parallel = FALSE
)

Arguments

counts_data	a counts data frame of rows in genes and columns in samples
group_list	a list ordered by samples in counts_data
test_group	the name of the numerator level for the fold change (Test group)
control_group	the name of the denominator level for the fold change (Control group)
dir	a directory to store results
parallel	if FALSE, no parallelization. if TRUE, parallel execution using BiocParallel

Value

a csv file and a DEG_container ob

Examples

## Not run: 
deg_run(counts_input,group_list,test_group = "T", control_group = "C",dir = tempdir())

## End(Not run)

xiayh17/RNAseqStat documentation built on June 16, 2022, 11:51 a.m.