October 2019
Intermediate to advanced
316 pages
9h 45m
English
Content preview from R Bioinformatics Cookbook
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How it works...
The code is a database lookup on, specifically, the Rattus norvegicus Ensembl Database through the relevant package. The process is similar to that for PFAM domain searches:
- We use the EnsemblDB package-specific hasProteinData() function to check whether the database has the information we need. If the output is TRUE, we're good:
## [1] TRUE
- We again build a list of genes of interest—here, I pull the list from the database, but these IDs can come from anywhere.
- Finally, we search the database with the genes of interest as a key. Note that we need the GeneIdFilter() function wrapper and the columns argument to select which data we want to return. This will result in a data frame with the following information:
## TXBIOTYPE ...
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