annotatePeaks-methods: annotatePeaks

In sheng-liu/SeqData: A data structure and four simple tools build upon it for sequencing data analysis

Description

Annotate peaks with internal or user provided annotation file.

Usage

## S4 method for signature 'SeqData,missing'
annotatePeaks(obj, annotationFile = character(0),
  feature = character(0), distance.max = 4000, description = character(0))

Arguments

obj	An SeqData Object.
distance.max	maximum peak-to-feature distance used to locate features.
description	Optional. User can input short desciption for the output file, it will show up in the file name of the output file.
feature=c("gene","erv","repeats","transposon")	including all features that are available in getFeatureAnnotation function. Note gene, exon, transcripts and tss are processed the same as gene.
peakTable	Full path to results "peakTable.csv" from findPeaks.

Details

It answers what gene are enriched with this protein/histone mark. Back end it is assaying which peak position overlaps with tss position by using "nearest" function from GenomicRanges package. It can annotate not just peaks find by annotatePeaks, but whatever RleViews is stored in coverageView.

Value

a targetTable.

Usage

annotatePeaks( obj,annotationFile=character(0),feature=character(0),distance.max=4000,description=character(0))

Examples

#if you have setup bamFile and annotationFile slot
#annotatePeaks(obj)

#if you want to use internal annotation file (feature)
#annotatePeaks(obj, feature="gene")

# specify another annotation file
#annotatePeaks(obj,annotationFile)

# use peakTable output from findPeaks
#annotatePeaks(peakTable, feature)

# use peakTable and annotation file
#annotatePeaks(peakTable,annotationFile)

sheng-liu/SeqData documentation built on May 29, 2019, 9:22 p.m.