makeBed: Create a BED file from an output of ZIMHMM

In plbaldoni/ZIMHMM: Improved Detection of Epigenomic Marks With Mixed Effects HMMs

Description

'makeBed()' imports the output from 'ZIMHMM()' and a RangedSummarizedExperiment object dataset to create a BED file to be used in downstream analyses.

Usage

makeBed(output, data, file, tracklabel = "User Track")

Arguments

output	An output from 'ZIMHMM()'
data	A RangedSummarizedExperiment object with the same assay used in 'ZIMHMM()'
file	The full path and name of the output file (e.g. './example.bed')
tracklabel	Optional label for the track (default is 'User Track')

Value

A GRanges object with consensus peaks.

Author(s)

Pedro L. Baldoni, [e-mail]

References

https://github.com/plbaldoni/mixHMM

Examples

data(Huvec)
ChIP = SummarizedExperiment::assay(Huvec,'ChIP')
Control = log(SummarizedExperiment::assay(Huvec,'Control')+1)
offset = matrix(0,nrow = nrow(ChIP),ncol = ncol(ChIP))
## Not run: output = ZIMHMM(ChIP = ChIP,Control = Control,offset = offset,random = 'intercept',control = controlPeaks())
## Not run: makeBed(output,data = Huvec,file = './H3K36me3.bed')

plbaldoni/ZIMHMM documentation built on Dec. 5, 2019, 11:43 p.m.