gene_tr_id {BANDITS} | R Documentation

## Gene-transcript matching

### Description

Gene-transcript matching

### Arguments

`gene_tr_id` | a `data.frame` containing the matching between gene (1st column) and transcript identifiers (2nd column). The gtf file used was downloaded from the ARMOR github repository here.

### Author(s)

Simone Tiberi simone.tiberi@uzh.ch

### Examples

    # Compute the 'gene_tr_id' object from the gtf file as shown in the vignettes,
    # see: browseVignettes("BANDITS").
    # suppressMessages(library(GenomicFeatures))
    # tx = makeTxDbFromGFF("Homo_sapiens.GRCh38.93.1.1.10M.gtf")
    # ss = unlist(transcriptsBy(tx, by="gene"))
    # gene_tr_id_gtf = data.frame(gene_id = names(ss), transcript_id = ss$tx_name )
    # gene_tr_id_gtf = gene_tr_id_gtf[ rowSums( is.na(gene_tr_id_gtf)) == 0, ] # remove eventual NA's
    # gene_tr_id_gtf = unique(gene_tr_id_gtf) # remove eventual duplicated rows

    # load the Gene-Transcript data.frame and visualize its top
    data(gene_tr_id, package = "BANDITS")
    head(gene_tr_id)

[Package BANDITS version 1.2.3 Index]