Run DEseq2

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

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

if (FALSE) {
deg_DESeq2(counts_input,group_list,
          test_group = "T", control_group = "C", qc = TRUE,
           x = "log2FoldChange", y = "pvalue",
           dir = tempdir(), prefix = "2-DEG_DEseq2")
}