run all step in default setting

Only need count data, group, OrgDb, dir

runAll(
  count_data,
  group_list,
  OrgDb = "org.Hs.eg.db",
  dir = ".",
  test_group = "T",
  control_group = "C",
  parallel = FALSE
)

Arguments

count_data

a counts data frame of rows in genes and columns in samples

group_list

a list ordered by samples in counts_data

OrgDb

OrgDb

dir

a directory to store results

test_group

which one is test group in your group_list

control_group

which one is control group in your group_list

parallel

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

Value

a dir contains all results

Examples

if (FALSE) {
runAll(count_data = counts_input, group_list = group_list, OrgDb = 'org.Hs.eg.db', dir = tempdir())
}