makeBed: Create a BED file from an output of mixHMM

In plbaldoni/mixHMM: Differential Peak Calling via Hidden Markov Model With Mixture of Negative Binomial Distributions

Description

'makeBed()' imports the output from 'mixHMM()' 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 'mixHMM()'
data	A RangedSummarizedExperiment object with the same assay used in 'mixHMM()'
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 differential peak calls

Author(s)

Pedro L. Baldoni, [e-mail]

References

https://github.com/plbaldoni/mixHMM

Examples

data(H3K36me3)
ChIP = SummarizedExperiment::assay(H3K36me3)
offset = ZIMHMM::createOffset(ChIP,method = 'loess',span = 1)
group = c(1,1,1,2,2,2,3,3,3)
B = 2^(length(unique(group)))-2
## Not run: output = mixHMMConstr(ChIP,Control=NULL,offset,group,B,control = controlPeaks())
## Not run: makeBed(output,data = H3K36me3,file = './H3K36me3.bed')

plbaldoni/mixHMM documentation built on Nov. 8, 2019, 8:05 p.m.