loadCountData {CSSQ}R Documentation

Load count data from input file.

Description

It converts input count file and a bed file regions into a RangedSummarizedExperiment-class object.

Usage

loadCountData(countFile, regionBed, sampleInfo)

Arguments

countFile

A path to file containing the count data for the dataset. This should be a tab separated file sample names as header.

regionBed

A bed file containing the list of regions that are being analyzed.

sampleInfo

Object from preprocessData containing sample information.

Value

RangedSummarizedExperiment-class object containing the region information, sample information and the count data.

Examples

countData <- loadCountData(system.file("extdata", "sample_count_data.txt", 
package="CSSQ",mustWork = TRUE),system.file("extdata", "chr19_regions.bed",
package="CSSQ"),
read.table(system.file("extdata", "sample_info.txt", package="CSSQ",
mustWork = TRUE),
sep="\t",header=TRUE))
countData

[Package CSSQ version 1.5.1 Index]