[BioC] GRanges list and reduce function
Asma rabe
asma.rabe at gmail.com
Fri Aug 15 12:20:30 CEST 2014
Hi ,
I need a Granges object with exons data for few chromosomes, i got Granges
list of transcripts and their exons as follows:
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
txdb<-TxDb.Hsapiens.UCSC.hg19.knownGene
tx_Exons<-exonsBy(txdb)
1-How to use reduce on Granges list?how to get the unique exons only and
exclude redundant exons?
2-How to select exons of certain chromosomes only ex: chr10? i tried the
following but i wonder why i got GRnages list with empty Grange lists??
chr10<-tx_Exons[seqnames(tx_Exons)=="chr10",]
>chr10
GRangesList of length 80922:
$1
GRanges with 0 ranges and 3 metadata columns:
seqnames ranges strand | exon_id exon_name exon_rank
<Rle> <IRanges> <Rle> | <integer> <character> <integer>
$2
GRanges with 0 ranges and 3 metadata columns:
seqnames ranges strand | exon_id exon_name exon_rank
$3
GRanges with 0 ranges and 3 metadata columns:
seqnames ranges strand | exon_id exon_name exon_rank
...
<80919 more elements>
---
seqlengths:
chr1 chr2 ... chrUn_gl000249
249250621 243199373 ... 38502
> length(chr10)
[1] 80922
> length(tx_Exons)
[1] 80922
Thank you
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