run_DESeq2: Basic produce of DESeq2

In xiayh17/RNAseqStat: A Pipeline to Process RNAseq Data

Basic produce of DESeq2

Description

A basic function to get data and produce results of DESeq2

Usage

run_DESeq2(
  counts_data,
  group_list,
  test_group,
  control_group,
  qc = TRUE,
  dir = ".",
  prefix = "2-DEG_DEseq2",
  parallel = FALSE
)

Arguments

counts_data	a counts data frame of rows in genes and columns in samples
group_list	a character vector 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)
qc	qc plots
dir	a directory to store results
prefix	a prefix of file names in this step
parallel	if FALSE, no parallelization. if TRUE, parallel execution using BiocParallel

Value

a DEG data frame

Examples

## Not run: 
run_DESeq2(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.