annotatedPeak: Annotated Peaks

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

Annotated Peaks

Description

TSS annotated putative STAT1-binding regions that are identified in un-stimulated cells using ChIP-seq technology (Robertson et al., 2007)

Usage

annotatedPeak

Format

GRanges with slot start holding the start position of the peak, slot end holding the end position of the peak, slot names holding the id of the peak, slot strand holding the strands and slot space holding the chromosome location where the peak is located. In addition, the following variables are included.

list("feature")

id of the feature such as ensembl gene ID

list("insideFeature")

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

list("distancetoFeature")

distance to the nearest feature such as transcription start site

list("start_position")

start position of the feature such as gene

list("end_position")

end position of the feature such as the gene

Details

obtained by data(TSS.human.GRCh37)

data(myPeakList)

annotatePeakInBatch(myPeakList, AnnotationData = TSS.human.GRCh37, output="b", multiple=F)

Examples

data(annotatedPeak)
head(annotatedPeak, 4)  # show first 4 ranges
if (interactive() || Sys.getenv("USER")=="jianhongou") {
y = annotatedPeak$distancetoFeature[!is.na(annotatedPeak$distancetoFeature)]
hist(as.numeric(as.character(y)), 
     xlab="Distance To Nearest TSS", main="", breaks=1000, 
ylim=c(0, 50), xlim=c(min(as.numeric(as.character(y)))-100, 
max(as.numeric(as.character(y)))+100))
}

jianhong/ChIPpeakAnno documentation built on Feb. 2, 2024, 3:26 p.m.