getAllPeakSequence

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Obtain genomic sequences around the peaks

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

Keywords
misc
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.

Aliases
  • getAllPeakSequence
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")
Documentation reproduced from package ChIPpeakAnno, version 3.6.5, License: GPL (>= 2)

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