Dear all, I'm trying to get exon by exon data matrix. I can download the data either directly from the website or through the R package.
For example here is simple single sample example:
download_study("DRP001219", type = "rse-exon", outdir="./data/") load(file.path( "./data/rse_exon.Rdata")) count = assays(rse_exon)$counts
Here is how the data matrix look like. For example here is one for KRAS which should have 6 exons the most, however this is how the annotation look like. Anyone know how I can convert or annotate this with exon info specically for version 2? thanks.
DRR014113 ENSG00000133703.11 78483 ENSG00000133703.11 4095 ENSG00000133703.11 5518 ENSG00000133703.11 388 ENSG00000133703.11 2350 ENSG00000133703.11 5462 ENSG00000133703.11 1972 ENSG00000133703.11 2725 ENSG00000133703.11 235 ENSG00000133703.11 1108 ENSG00000133703.11 2495 ENSG00000133703.11 0 ENSG00000133703.11 0