gene_tr_id {BANDITS} | R Documentation |
Gene-transcript matching
gene_tr_id |
a |
Simone Tiberi simone.tiberi@uzh.ch
# 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)