run DEG

run DEG module in limma, DESeq2 and edgeR

deg_run(
  counts_data,
  group_list,
  test_group = "T",
  control_group = "C",
  dir,
  parallel = FALSE
)

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

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)

dir

a directory to store results

parallel

if FALSE, no parallelization. if TRUE, parallel execution using BiocParallel

Value

a csv file and a DEG_container ob

Examples

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