DESeq2_resolve: Basic produce of DESeq2

In xiayh17/RNAseqStat2: A Pipeline to Process RNAseq Data

Basic produce of DESeq2

Description

A basic function to get data and produce results of DESeq2

Usage

DESeq2_resolve(
  counts_data,
  group_list,
  case_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
case_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: 
DESeq2_resolve(counts_input, group_list,case_group = "T", control_group = "C", dir = tempdir())

## End(Not run)

xiayh17/RNAseqStat2 documentation built on May 27, 2023, 12:13 p.m.