utr3.danRer10: 3'UTR annotation for danRer10 obtained from utr3Annotation

In InPAS: InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

Description

3'UTR annotation obtained from utr3Annotation by TxDb.Drerio.UCSC.danRer10.refGene and org.Dr.eg.db

Usage

data(utr3.danRer10)

Format

GRanges with slot start holding the start position of the 3'UTR, slot end holding the end position of the 3'UTR, slot names holding transcripts and gene names of 3'UTR, slot seqnames holding the chromosome location where the 3'UTR is located and slot strand for strand of 3'UTR. In addition, the following variables are included.

feature

should be unknown or proximalCP_XXXXXXXX

id

should be utr3 or next.exon.gap

exon

exon id

transcript

trnscript id

gene

entriz gene id

symbol

gene symbol

Details

used in the examples Annotation data obtained by: library(TxDb.Drerio.UCSC.danRer10.refGene)

library(org.Dr.eg.db)

utr3Annotation(TxDb.Drerio.UCSC.danRer10.refGene, "org.Dr.egSYMBOL")

Value

an object of GRanges.

Examples

    data(utr3.danRer10)
    head(utr3.danRer10)

InPAS documentation built on Nov. 8, 2020, 5:03 p.m.