Deleted:How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
1
2
Entering edit mode
14 months ago
Pratik ▴ 850

Hello Biostars Community,

How do I build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts? Basically, I am trying to overlap CDS coordinates from a TxDb object to CpG Loci from a GRanges object and make sure these CDS coordinates are grouped by gene transcripts.

The reproducible data is within the SesameData package used in the sesame package.


I am trying to create a txns GRangesList similar to the one below:

library(sesameData)
genomeInfo.mm10 <- sesameData::sesameDataGet('genomeInfo.mm10')
txns.reference <- genomeInfo.mm10$txns

I am trying to do this for the mm39 assembly, but for the sake of providing a reproducible example, I'll only include an mm10 working example.

This is how far I have gotten:

MM285.mm10.manifest <- sesameData::sesameDataGet('MM285.mm10.manifest')
mm10.txdb <- GenomicFeatures::makeTxDbFromEnsembl(organism = "Mus musculus", release = 102)
seqlevelsStyle(mm10.txdb) <- "UCSC"
txns.reproducible.example <- cdsByOverlaps(x = mm10.txdb, ranges =  MM285.mm10.manifest, columns = c("CDSSTART","CDSEND"))

The txns.reproducible.example is a GRanges object not a GRangesList, and it does not contain NAMES of the gene transcripts as txns.refernce does. I have tried many ways, but no success yet.

I would appreciate help from anyone. Thank you in advance!

-Pratik

GenomicFeatures GenomicRanges • 349 views
ADD COMMENT
This thread is not open. No new answers may be added
Traffic: 1228 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6