getGeneSeq: Get gene sequence using the biomaRt package

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

Get gene sequence using the biomaRt package

Description

Get gene sequence using the biomaRt package

Usage

getGeneSeq(LocationParameters, mart)

Arguments

LocationParameters	c(ensembl_gene_id, distance from the peak to the transcription start site of the gene with the above ensemblID, upstream offset from the peak, downstream offset from the peak, Gene Start, Gene End)
mart	see useMart of bioMaRt package for details

Value

a list with the following items

feature_id	ensemble gene ID
distancetoFeature	distance from the peak to the transcriptionstart site of the gene with the above ensembl gene ID
upstream	upstream offset from the peakStart
downstream	downstream offset from the peakEnd
seq	sequence obtained around the peak with above upstream and downstream offset

Note

internal function not intended to be called directly by users

Author(s)

Lihua Julie Zhu

Examples

if (interactive())
{
mart <- useMart(biomart="ensembl", dataset="drerio_gene_ensembl")
LocationParameters =c("ENSDARG00000054562",400, 750, 750,40454140,40454935)
getGeneSeq(LocationParameters, mart)

LocationParameters =c("ENSDARG00000054562",752, 750, 750,40454140,40454935)
getGeneSeq(LocationParameters, mart)
 
LocationParameters =c("ENSDARG00000054562",750, 750, 750,40454140,40454935)
getGeneSeq(LocationParameters, mart)
 
 LocationParameters =c("ENSDARG00000054562",-2, 750, 750,40454140,40454935)
 getGeneSeq(LocationParameters, mart)

 LocationParameters =c("ENSDARG00000054562",0, 750, 750,40454140,40454935)
 getGeneSeq(LocationParameters, mart)
 
 LocationParameters =c("ENSDARG00000054562",2, 750, 750,40454140,40454935)
 getGeneSeq(LocationParameters, mart) 
 
 LocationParameters =c("ENSDARG00000054562",1000, 750, 750,40454140,40454935)
 getGeneSeq(LocationParameters, mart)
}

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