Entering edit mode
2.1 years ago
yangliu326459
▴
30
Hi,
I want to use a txdb annotation database to find out the genes that have no overlap with others. So I first get all genes locus:
library(GenomicFeatures)
txdb <- loadDb("gencode.v40.annotation.sqlite")
gene <- genes(txdb)
gene
## GRanges object with 2450 ranges and 1 metadata column:
## seqnames ranges strand | gene_id
## <Rle> <IRanges> <Rle> | <character>
## ENSG00000000003.15 chrX 100627108-100639991 - | ENSG00000000003.15
## ENSG00000000005.6 chrX 100584936-100599885 + | ENSG00000000005.6
## ENSG00000001497.18 chrX 65438549-65534810 - | ENSG00000001497.18
## ENSG00000002586.20 chrX 2691187-2741309 + | ENSG00000002586.20
## ENSG00000003096.14 chrX 117897813-118117340 - | ENSG00000003096.14
## ... ... ... ... . ...
## ENSG00000289575.1 chrX 87723928-87728679 - | ENSG00000289575.1
## ENSG00000289591.1 chrX 146854539-146954956 + | ENSG00000289591.1
## ENSG00000289596.1 chrX 13085729-13086383 + | ENSG00000289596.1
## ENSG00000289620.1 chrX 1661815-1662306 + | ENSG00000289620.1
## ENSG00000289708.1 chrX 36984358-36984493 + | ENSG00000289708.1
## -------
## seqinfo: 1 sequence from an unspecified genome; no seqlengths
Next, I want to find out which genes have no overlap with others.
So the question becomes how to find ranges that overlap other ranges within gene GRanges object.
I can achieve this by using for looping, but it is too inefficient.
I would be thankful for any help to achieve this efficiently with a function or anything else!
Have you checked at this ? https://sa-lee.github.io/plyranges/reference/ranges-overlaps-self.html
Thanks for your reply!! And I have tried this package, but it does not solve my problem. So I adopt the inefficient ways to solve this problem.