getAllPeakSequence: Obtain genomic sequences around the peaks

Description Usage Arguments Value Author(s) References Examples

View source: R/getAllPeakSequence.R

Description

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

Usage

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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

GRanges object with annotation information.

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

Author(s)

Lihua Julie Zhu, Jianhong Ou

References

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

Examples

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#### 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")

ChIPpeakAnno documentation built on April 1, 2021, 6:01 p.m.