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
