runAll: run all step in default setting

In xiayh17/RNAseqStat: A Pipeline to Process RNAseq Data

run all step in default setting

Description

Only need count data, group, OrgDb, dir

Usage

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

## Not run: 
runAll(count_data = counts_input, group_list = group_list, OrgDb = 'org.Hs.eg.db', dir = tempdir())

## End(Not run)

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