maser: Create a maser object by importing rMATS splicing events.

In DiogoVeiga/maser: Mapping Alternative Splicing Events to pRoteins

Description

Create a maser object by importing rMATS splicing events.

Usage

maser(path, cond_labels, ftype = c("ReadsOnTargetAndJunctionCounts",
  "JunctionCountOnly", "JCEC", "JC"))

Arguments

path	a character specifiying the folder containing rMATS output files.
cond_labels	a character vector of length 2 describing labels for experimental conditions.
ftype	a character indicating the rMATS file type. Possible values are c("ReadsOnTargetAndJunctionCounts", "JunctionCountOnly", "JCEC", "JC").

Details

This function creates a maser object by importing rMATS output. ftype indicates which rMATS files to import. ReadsOnTargetandJunction or JunctionCountOnly are used in rMATS 3.2.5 or lower. Newer versions (>4.0.1) use "JCEC" or "JC" nomenclature.

Value

A maser object.

Examples

path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))

DiogoVeiga/maser documentation built on Feb. 10, 2022, 10:10 a.m.