loadCountData: Load count data from input file.

In CSSQ: Chip-seq Signal Quantifier Pipeline

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

CSSQ documentation built on Nov. 8, 2020, 6:47 p.m.