ChIPpeakAnno (version 3.6.5)

getAllPeakSequence: Obtain genomic sequences around the peaks

Description

Obtain genomic sequences around the peaks leveraging the BSgenome and biomaRt package

Usage

getAllPeakSequence(myPeakList, upstream = 200L, downstream = upstream,  genome, AnnotationData)

Arguments

myPeakList

An object of GRanges: See example below

upstream

upstream offset from the peak start, e.g., 200

downstream

downstream offset from the peak end, e.g., 200

genome

BSgenome object or mart object. Please refer to available.genomes in BSgenome package and useMart in bioMaRt package for details

AnnotationData

RangedData used if mart object is parsed in which can be obtained from getAnnotation with featureType="TSS". For example, data(TSS.human.NCBI36), data(TSS.mouse.NCBIM37), data(GO.rat.RGSC3.4) and data(TSS.zebrafish.Zv8). If not supplied, then annotation will be obtained from biomaRt automatically using the mart object

Value

GRanges with slot start holding the start position of the peak, slot end holding the end position of the peak, slot rownames holding the id of the peak and slot seqnames holding the chromosome where the peak is located. In addition, the following variables are included:

upstream

upstream offset from the peak start

downstream

downstream offset from the peak end

sequence

the sequence obtained

References

Durinck S. et al. (2005) BioMart and Bioconductor: a powerful link between biological biomarts and microarray data analysis. Bioinformatics, 21, 3439-3440.

Examples

#### use Annotation data from BSgenome
peaks <- GRanges(seqnames=c("NC_008253", "NC_010468"),
                 IRanges(start=c(100, 500), end=c(300, 600), 
                         names=c("peak1", "peak2")))
library(BSgenome.Ecoli.NCBI.20080805)
seq <- getAllPeakSequence(peaks, upstream=20, downstream=20, genome=Ecoli)
write2FASTA(seq, file="test.fa")