summarizePeaks: Summarize peak calls and optionally create a BED 6+3 file in...

Description Usage Arguments Value Author(s) References Examples

View source: R/summarizePeaks.R

Description

'summarizePeaks()' imports the output from 'mixNBHMM()' and outputs a set of differential peaks for a given FDR control threshold (or from the Viterbi sequence of HMM states).

Usage

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summarizePeaks(
  object,
  type = "viterbi",
  name = NULL,
  path = NULL,
  description = NULL
)

Arguments

object

a mixNBHMMDataSet

type

either 'viterbi' (default) or an FDR control threshold (e.g. 0.05)

name

either NULL (default) or the name (without extension) for the outputfiles (e.g. 'mixNBHMM')

path

either NULL (default) or a character string with the path where the output files will be saved (e.g. '~/home/')

description

either NULL (default) or a character string to be used as header description in the output files (e.g. 'Viterbi peaks')

Value

A GRanges object with differential peak calls in BED 6+3 format

Author(s)

Pedro L. Baldoni, pedrobaldoni@gmail.com

References

https://github.com/plbaldoni/mixNBHMM

Examples

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data(ENCODE)
ENCODE <- createOffset(object = ENCODE,type = 'loess',span = 1)
## Not run: ENCODE <- mixNBHMM(object = ENCODE,control = controlEM())
## Not run: summarizePeaks(object = ENCODE, type = 'viterbi', name = 'mypeaks',
path = '~/mypeaks/', description = 'Viterbi peaks')
## End(Not run)

plbaldoni/mixNBHMM documentation built on Dec. 24, 2019, 1:31 p.m.