createQseaSet {qsea} | R Documentation |
This method prepares the qseaSet object, and prepares genome wide bins. Coverage and normalization parameters are added in succeeding functions.
createQseaSet(sampleTable,BSgenome, chr.select,Regions, window_size=250 )
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 |
An object of class qseaSet, containing the sample and genome information.
Mathias Lienhard
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)