deg_limma: Run limma

In xiayh17/RNAseqStat: A Pipeline to Process RNAseq Data

Run limma

Description

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

Usage

deg_limma(
  counts_data,
  group_list,
  test_group,
  control_group,
  x,
  y,
  dir = ".",
  prefix = "2-DEG_limma"
)

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)
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

deg_limma(counts_input,group_list,
          test_group = "T", control_group = "C",
           x = "logFC", y = "P.Value",
           dir = tempdir(), prefix = "2-DEG_limma")

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