example: Simulation of MeDIP seq QSEA set

Description Usage Arguments Details Value Author(s) See Also Examples

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

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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

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qsea documentation built on Nov. 8, 2020, 8:28 p.m.