getAllPeakSequence: Obtain genomic sequences around the peaks

In LihuaJulieZhu/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

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	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

#### 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")

LihuaJulieZhu/ChIPpeakAnno documentation built on Aug. 5, 2020, 12:02 a.m.