example: Simulation of MeDIP seq QSEA set

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

Simulation of MeDIP seq QSEA set

Description

Creates a example qseaSet object by sampling reads for simulated Tumor and Normal samples. Number of replicates, sequencing depth and fraction of background reads can be specified.

Usage

getExampleQseaSet(CpG=TRUE,CNV=TRUE,repl=2, 
    doSampling=TRUE,enrichmentAnalysis=TRUE, expSamplingDepth=50000, 
    bgfraction=.1)

Arguments

CpG	if TRUE CpG density is added to the object
CNV	if TRUE CNV are emulated for the tumor samples
repl	number of replicates for tumor and normal samples
doSampling	if TRUE, read counts are sampled and added to the object
enrichmentAnalysis	if TRUE, parameters for enrichment profiles are added
expSamplingDepth	expected value of sequencing depth
bgfraction	fraction of background reads

Details

The function creates an example and test qseaSet object for an toy example genome (one chromosome, 50kb) with 500 bases windows.

Value

The qseaSet object

Author(s)

Mathias Lienhard

See Also

createQseaSet()

Examples

qs=getExampleQseaSet()

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