methylKit (version 0.9.5)

filterByCoverage: Filter methylRaw and methylRawList object based on read coverage

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

# NOT RUN {
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)
# }