Basic produce of DESeq2

A basic function to get data and produce results of DESeq2

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

if (FALSE) {
run_DESeq2(counts_input, group_list,test_group = "T", control_group = "C", dir = tempdir())
}