gene_tr_id: Gene-transcript matching

In SimoneTiberi/BANDITS: BANDITS: Bayesian ANalysis of DIfferenTial Splicing

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 [e-mail]

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)

SimoneTiberi/BANDITS documentation built on Nov. 15, 2023, 2:35 p.m.