DJEimport: DJEimport: Construction of junction expression matrix

In MauerLab/DJExpress: An integrated application for differential splicing analysis and visualization

Description

Uses sample-level junction quantification files to construct expression matrix. Returns output object for DJEannotate.

Usage

DJEimport(
  workDir = NULL,
  data.type = c("sample", "matrix"),
  aligner = c("STAR", "other"),
  min.expressed = 3
)

Arguments

workDir	path to folder where individual junction quantification files (e.g. from STAR alignment) are located. This folder should only contain junction quantification files.
data.type	One of c("sample", "matrix"), indicating whether the input files are matrices per individual samples or joint into a single expression matrix.
aligner	One of c("STAR", "other"), indicating the alignment tool used to produce junction quantification. Only used if data.type = "matrix". If "other" is indicated, files in workDir path should contain junction IDs (with the format chr:start:end:strand) in the first column read counts in the second column.
min.expressed	Numeric. Minimal number of junction reads to be considered expressed in sample. Default is 3 reads.

Value

Matrix of samples as columns and junction quantifications as rows and associated matrix with genomic coordinates.

Examples

in.file <- system.file("extdata", "junct.quant", package = "DJExpress")
out.file <- DJEimport(in.file, aligner="STAR")

MauerLab/DJExpress documentation built on Jan. 1, 2022, 12:57 p.m.