addPatternDensity: Infer sequence pattern density values and add to qseaSet...

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

Infer sequence pattern density values and add to qseaSet object

Description

This function estimates the average occurrences of a sequence pattern (such as CpG dinucleotides) within the overlapping sequencing fragments for each genomic window

Usage

addPatternDensity(qs, pattern,name, fragment_length, fragment_sd,
patternDensity, fixed=TRUE, masks=c("AGAPS","AMB", "RM", "TRF")[1:2])

Arguments

qs	a qseaSet object
pattern	actual sequence of the pattern (e.g. “CG”)

,

name	a name for the sequence pattern(e.g. “CpG”)

,

fragment_length	the average fragment length to be assumed for pattern density estimation. If omitted, this parameter is taken from the qseaSet object.
fragment_sd	the standard deviation of fragment length to be assumed for pattern density estimation. If omitted, this parameter is taken from the qseaSet object.
patternDensity	this parameter alternatively allows to specify the pattern density manually. In this case, please provide a numerical vector, containing a value (greater than 0) for each genomic window.
fixed	if FALSE, an IUPAC ambiguity code in the pattern can match any letter in the reference genome that is associated with the code, and vice versa.
masks	names of the BSgenome masks to be active.

Value

The function returns the qseaSet object, extended by the pattern density for all genomic windows

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")
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)
qseaSet=addPatternDensity(qseaSet, "CG", name="CpG", fragment_length=300)

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