How many transcripts?
Remember in the video how we discovered the length of the exons in one of the transcripts of our gene of interest? It is your turn to find out how many transcripts the gene ABCD1 has. You can find out by using:
transcriptsBy(x, by = "gene")
Once you get all the transcripts by gene, you can then select any gene by its id. The gene id of ABCD1 is 215. A little tip to select the information on a specific gene is to use back-tick marks around the gene id, for example transcripts$`215`.
This exercise is part of the course
Introduction to Bioconductor in R
Exercise instructions
- Load the human transcripts DB to
hg. - Pre-filter chromosome X using
seqlevels(). - Get all transcripts in
hgby"gene", store results inhg_chrXt, and print it. - Select gene
`215`fromhg_chrXtusing$.
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Load the human transcripts DB to hg
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
hg <- ___
# Prefilter chromosome X "chrX" using seqlevels()
___(___) <- c(___)
# Get all transcripts by gene and print it
hg_chrXt <- transcriptsBy(___, by = ___)
hg_chrXt
# Select gene `215` from the hg_chrXt
___$___