MEDIPS (version 1.22.0)

MEDIPS.seqCoverage: The function identifies the number of CpGs (or any other predefined sequence pattern) covered by the given short reads.

Description

The main idea of the sequence pattern coverage analysis is to test the number of CpGs (or any other predefined sequence pattern) covered by the given short reads and to test the depth of coverage.

Usage

MEDIPS.seqCoverage(file = NULL, BSgenome = NULL, pattern = "CG", extend = 0, shift = 0, uniq = 1e-3, chr.select = NULL, paired = F, bwa=FALSE)

Arguments

file

Path and file name of the input data

BSgenome

The reference genome name as defined by BSgenome

pattern

defines the sequence pattern, e.g. CG for CpGs.

extend

defines the number of bases by which the region will be extended before the genome vector is calculated. Regions will be extended along the plus or the minus strand as defined by their provided strand information. Please note, the extend and shift parameter are mutual exclusive.

shift

defines the number of bases by which the region will be shifted before the genome vector is calculated. Regions will be shifted along the plus or the minus strand as defined by their provided strand information. Please note, the extend and shift parameter are mutual exclusive.

uniq

The uniq parameter determines, if all reads mapping to exactly the same genomic position should be kept (uniq = 0), replaced by only one representative (uniq = 1), or if the number of stacked reads should be capped by a maximal number of stacked reads per genomic position determined by a poisson distribution of stacked reads genome wide and by a given p-value (1 > uniq > 0) (deafult: 1e-3). The smaller the p-value, the more reads at the same genomic position are potentially allowed.

chr.select

specify a subset of chromosomes for which the saturation analysis is performed.

paired

option for paired end reads

bwa

Indicates, if the alignment file has been generated by bwa (default=FALSE). Enabling bwa allows that the first mate of pairs can be the 'left' or the 'right' mate.

Examples

library(MEDIPSData)
library(BSgenome.Hsapiens.UCSC.hg19)
bam.file.hESCs.Rep1.MeDIP = system.file("extdata", "hESCs.MeDIP.Rep1.chr22.bam", package="MEDIPSData")

cr = MEDIPS.seqCoverage(file=bam.file.hESCs.Rep1.MeDIP, BSgenome="BSgenome.Hsapiens.UCSC.hg19", pattern="CG", extend=250, shift=0, uniq=1e-3, chr.select="chr22")