annotate.macs.output: annotate MACS peaks using ChIPpeakAnno

In drmjc/macsR: Facilitate analysis of MACS results.

Description

This compares the BED regions from running MACS to the nearest ENSEMBL Gene, and to CpG islands. This uses annotatePeakInBatch from ChIPpeakAnno, which has a very loose definition of close, ie within 0.5Mb.

Usage

  annotate.macs.output(dir,
    genome = c("hg19", "hg18", "mm9", "rn4"), tss = TRUE,
    cpg = TRUE)

Arguments

dir	the path to a MACS peaks.annot directory
genome	one of ‘hg18’, or ‘hg19’
tss	logical: if TRUE, then annotate peaks with the nearest TSS
cpg	logical: if TRUE, then annotate peaks with the nearest CpG islands

Details

This uses pre-built CpG island definitions downloaded from UCSC.

Value

nothing. it writes a <prefix>_peaks_annot.xls file. There are a block of columns for the nearest TSS, and a block for CpG islands. To interpret the new columns, see annotatePeakInBatch. These columns include:

Ensembl ID	The Ensembl Gene ID of the nearest TSS
GeneSymbol	The GeneSymbol assigned to the ENSG
start_position	start position of the feature: TSS or CpG
end_position	end position of the feature: TSS or CpG
strand	1 or + for positive strand and -1 or - for negative strand where the feature is located
insideFeature	One of these keywords: upstream peak resides upstream of the feature downstream peak resides downstream of the feature inside peak resides inside the feature overlapStart peak overlaps with the start of the feature overlapEnd peak overlaps with the end of the feature includeFeature peak include the feature entirely
distancetoFeature	distance to the nearest feature. By default, the distance is calculated as the distance between the start of the binding site and the TSS that is the gene start for genes located on the forward strand and the gene end for genes located on the reverse strand.
shortestDistance	The shortest distance from either end of peak to either end the feature
fromOverlappingOrNearest	One of these keywords: NearestStart: indicates this feature's start (feature's end for features at minus strand) is closest to the peak start; Overlapping: indicates this feature overlaps with this peak although it is not the nearest feature start

Author(s)

Mark Cowley, 2012-03-01

Examples

## Not run: 
dir <- "./MACS/TAMR.H3k4Me3.vs.MCF7.H3k4Me3/"
annotate.macs.output(dir, "hg19")

## End(Not run)

drmjc/macsR documentation built on May 15, 2019, 2:23 p.m.