ChIP.promoter: ChIP.promoter

Description Usage Arguments Value Examples

View source: R/ChIP.promoter.R

Description

Get a GRanges with enhancer-positions

Usage

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ChIP.promoter(H3K4me3, TSS = NULL, ignorePeak = NULL, TSSpad = 2000,
  padding = 100, verbose = F)

Arguments

H3K4me3

A BED-df with H3k27ac-peak positions.

TSS

A data-frame from biomart, containing a bed-like structure of TSS's

ignorePeak

A BED-df with peak positions of an mark not associated with promoters (e.g. H3KK27ac). Can be a list.

TSSpad

Search-space for TSS-H3K4me3

padding

Extend peaks.

Value

A genomicRanges-object

Examples

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promoters <- ChIP.promoter(H3K4me3 = H3K4me3,TSS = TSS , ignorePeak = list(H3K4me1, H3K27ac), TSSpad = 1e3)
enhancers <- ChIP.enhancer(ignorePeak = H3K4me3,H3K27ac = H3K27ac, activePeak = H3K4me1)

robinweide/RHWlib documentation built on July 23, 2018, 4:13 a.m.