deg_DESeq2: Run DEseq2

In xiayh17/RNAseqStat: A Pipeline to Process RNAseq Data

Run DEseq2

Description

A integrated function for run DEseq2 in a counts data and return results files.

Usage

deg_DESeq2(
  counts_data,
  group_list,
  parallel = F,
  test_group,
  control_group,
  qc = TRUE,
  x,
  y,
  dir = ".",
  prefix = "2-DEG_DEseq2"
)

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
parallel	if FALSE, no parallelization. if TRUE, parallel execution using BiocParallel
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
x	which column is log FC
y	which column is P value
dir	a directory to store results
prefix	a prefix of file names in this step

Value

a directory contains figures and csv files and a deg data frame

Examples

## Not run: 
deg_DESeq2(counts_input,group_list,
          test_group = "T", control_group = "C", qc = TRUE,
           x = "log2FoldChange", y = "pvalue",
           dir = tempdir(), prefix = "2-DEG_DEseq2")

## End(Not run)

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