name2gidx: match gene name (symbol) to connected component index

In pkimes/spliceclust: Visualization and Clustering of Spliced Components

Description

Function matches a character string gene symbol to overlapping connected components according to annotations in txdb and txlist. Note to self: R follows copy-on-write semantics.

Usage

name2gidx(name, obj, txlist, txdb, orgdb)

Arguments

name	a character string specifying the gene of interest
obj	a GRangesList of connected component ranges, each name corresponding to the 'gene index'
txlist	a list of transcripts, e.g. exonsBy(txdb)
txdb	a transcript database, e.g. TxDb.Hsapiens.UCSC.hg19.knownGene (default = NULL)
orgdb	a organism database, e.g. org.Hs.eg.db (default = NULL)

Value

a data.frame with connected component IDs and overlapping transcript or gene names

Author(s)

Patrick Kimes

pkimes/spliceclust documentation built on Jan. 2, 2020, 4:44 a.m.