createQseaSet: Prepares a qseaSet Object

In MatthiasLienhard/qsea: IP-seq data analysis and vizualization

Prepares a qseaSet Object

Description

This method prepares the qseaSet object, and prepares genome wide bins. Coverage and normalization parameters are added in succeeding functions.

Usage

createQseaSet(sampleTable,BSgenome, chr.select,Regions, window_size=250 )

Arguments

BSgenome	name of BSgenome package
Regions	GRanges object. If specified, only selected regions are processed
chr.select	If specified, only selected chromosomes are processed
sampleTable	data.frame, containing at least 3 columns: the sample names (sample_name), paths to alignment or coverage file in sam/bam/wiggle/bigwig format (file_name), and one or more test condition(s) (group). Optionally it may contain a column with alignment or coverage files for CNV analysis, and further information in the samples that are of interest for the analysis.
window_size	size for the genome wide bins in base pairs

Value

An object of class qseaSet, containing the sample and genome information.

Author(s)

Mathias Lienhard

Examples

library("BSgenome.Hsapiens.UCSC.hg19")
bam_hESCs_1 = system.file("extdata", "hESCs.MeDIP.Rep1.chr22.bam", 
    package="MEDIPSData")
bam_hESCs_2 = system.file("extdata", "hESCs.MeDIP.Rep2.chr22.bam", 
    package="MEDIPSData")
samplesTable=data.frame(sample_name=paste0("hESCs_", 1:2), 
file_name=c(bam_hESCs_1,bam_hESCs_2), 
group=rep("hESC",2),stringsAsFactors=FALSE)
qs=createQseaSet(samplesTable, BSgenome="BSgenome.Hsapiens.UCSC.hg19", 
    chr.select="chr22", window_size=500)

MatthiasLienhard/qsea documentation built on March 22, 2023, 1:15 p.m.