addCNV: estimate CNV information and add to qseaSet object

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

estimate CNV information and add to qseaSet object

Description

This function adds information on Copy Number Variation (CNV) to the qseaSet object, which is used for normalization. Sample wise CNV information can either be provided, or estimated from input or enrichment sequencing data, by incorporating functions of the HMMcopy package.

Usage

addCNV(qs,file_name, window_size=1000000, paired=FALSE, fragment_length,cnv, 
mu=log2(c(1/2, 2/3, 1, 3/2,2,3)), normal_idx, plot_dir, MeDIP=FALSE, 
parallel=FALSE)

Arguments

qs	the qseaSet object
cnv	pre-computed CNV information for each sample. If provided, the following parameters are ignored
file_name	column name of the sample table for the sequencing files, from which CNV information are computed
window_size	window size for CNV analysis
paired	are files in file_name column paired end
fragment_length	for single end sequencing, provide the average fragment length
mu	a priori CNV levels of different states, parameter passed to HMMcopy
normal_idx	index of samples which are assumed to be CNV free. The median of these samples serves as "normal" CNV reference level, and CNV are computed relative to this reference level. By default, QSEA looks for samples with "normal" or "control" in its name.
plot_dir	If provided, detail CNV plots for each chromosome and each sample are created in the provided directory
MeDIP	If set TRUE, QSEA assumes that provided files are methylation enriched sequencing data. In this case, only fragments without CpG dinucleotides are considered. This option allows QSEA to infer CNV information from MeDIP or MDB seq experiments directly
parallel	Switch for parallel computing, using BiocParallel

Value

The qseaSet object, extended by the CNV information

Author(s)

Mathias Lienhard

See Also

HMMsegment

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")
sample_table=data.frame(sample_name=paste0("hESCs_", 1:2), 
    file_name=c(bam_hESCs_1,bam_hESCs_2), 
    group=rep("hESC",2), stringsAsFactors=FALSE)
qseaSet=createQseaSet(sampleTable=sample_table, 
        BSgenome="BSgenome.Hsapiens.UCSC.hg19", 
        chr.select="chr22", 
        window_size=500)

#this is an example for computing CNVs from MeDIP data. A very limited example
#however, since the samples do not contain CNVs.
qseaSet=addCNV(qseaSet, fragment_length=300, file_name="file_name", MeDIP=TRUE,
window_size=1000000)

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