filterByCoverage-methods: Filter methylRaw and methylRawList object based on read...

In fortunatobianconi/methylkit: DNA methylation analysis from high-throughput bisulfite sequencing results

Description

This function filters methylRaw and methylRawList objects. You can filter based on lower read cutoff or high read cutoff. Higher read cutoff is usefull to eliminate PCR effects Lower read cutoff is usefull for doing better statistical tests.

Usage

  filterByCoverage(methylObj,lo.count=NULL,lo.perc=NULL,hi.count=NULL,hi.perc=NULL)

Arguments

methylObj	a methylRaw or methylRawList object
lo.count	An integer for read counts.Bases/regions having lower coverage than this count is discarded
lo.perc	A double [0-100] for percentile of read counts. Bases/regions having lower coverage than this percentile is discarded
hi.count	An integer for read counts. Bases/regions having higher coverage than this is count discarded
hi.perc	A double [0-100] for percentile of read counts. Bases/regions having higher coverage than this percentile is discarded

Value

methylRaw or methylRawList object depending on input object

Examples

data(methylKit)

# filter out bases with covereage above 500 reads
filtered1=filterByCoverage(methylRawList.obj,lo.count=NULL,lo.perc=NULL,hi.count=500,hi.perc=NULL)

# filter out bases with cread coverage above 99.9th percentile of coverage distribution
filtered2=filterByCoverage(methylRawList.obj,lo.count=NULL,lo.perc=NULL,hi.count=NULL,hi.perc=99.9)

fortunatobianconi/methylkit documentation built on May 16, 2019, 1:51 p.m.