readMpsnakeAsDGEList: Read mpsnake output directory into a DGEList object

In bedapub/ribiosNGS: Utilities for next-generation sequencing data analysis in ribios

Read mpsnake output directory into a DGEList object

Description

Read mpsnake output directory into a DGEList object

Usage

readMpsnakeAsDGEList(dir, minReads = NULL)

Arguments

dir	Character string, path of mpsnake pipeline directory (or the results subdirectory).
minReads	NULL or tnteger, minimalistic read numbers for a sample to be considered. In case of NULL, no filtering is performed.

Value

A DGEList object containing counts, gene, and sample annotation

Examples

mpsnakeDir <- system.file("extdata/mpsnake-minimal-outdir", package="ribiosNGS")
mpsDgeList <- readMpsnakeAsDGEList(mpsnakeDir)

## equivalent
mpsnakeResDir <- system.file("extdata/mpsnake-minimal-outdir", "results",
  package="ribiosNGS")
mpsDgeList <- readMpsnakeAsDGEList(mpsnakeResDir)

bedapub/ribiosNGS documentation built on Feb. 10, 2025, 12:34 a.m.