utr3Annotation {InPAS} | R Documentation |
extract 3'UTR from a TxDb object. The 3'UTR is defined as the last 3'UTR fragment for each transcript and it will be cut if there is any overlaps with other exons.
utr3Annotation(txdb, orgDbSYMBOL, MAX_EXONS_GAP = 10000)
txdb |
an object of TxDb |
orgDbSYMBOL |
a string indicates org SYMBOL to entriz id map |
MAX_EXONS_GAP |
maximul exon gap for distal CP site |
return an object of GRanges with 7 metadata columns: feature (utr3, next.exon.gap, CDS), annotatedProximalCP (unknown, proximalCP_<coordinate>), exon (<transcript id>_<index>), transcript, gene (entrez_id), symbol, truncated (logical).
Jianhong Ou
if(interactive()){ library(TxDb.Mmusculus.UCSC.mm10.knownGene) library(org.Mm.eg.db) utr3Annotation(TxDb.Mmusculus.UCSC.mm10.knownGene, "org.Mm.egSYMBOL") }