unite-methods: unite methylRawList to a single table

In vd4mmind/methylkit: DNA methylation analysis from high-throughput bisulfite sequencing results

Description

This functions unites methylRawList object that only bases with coverage from all samples are retained. The resulting object is a class of methylBase

Usage

  unite(object,destrand=FALSE,min.per.group=NULL)

Arguments

object	a methylRawList object to be merged by common locations covered by reads
destrand	if TRUE, reads covering both strands of a CpG dinucleotide will be merged, do not set to TRUE if not only interested in CpGs (default: FALSE). If the methylRawList object contains regions rather than bases setting destrand to TRUE will have no effect.
min.per.group	an integer denoting minimum number of samples per replicate needed to cover a region/base. By default only regions/bases that are covered in all samples are united as methylBase object, however by supplying an integer for this argument users can control how many samples needed to cover region/base to be united as methylBase object. For example, if min.per.group set to 2 and there are 3 replicates per condition, the bases/regions that are covered in at least 2 replicates will be united and missing data for uncovered bases/regions will appear as NAs.

Value

a methylBase object

Examples

data(methylKit)
 ## Following
 my.methylBase=unite(methylRawList.obj)
 my.methylBase=unite(methylRawList.obj,destrand=TRUE)

vd4mmind/methylkit documentation built on May 3, 2019, 4:57 p.m.