October 2019
Intermediate to advanced
316 pages
9h 45m
English
Content preview from R Bioinformatics Cookbook
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I mentioned that the key to the recipe—in particular, the join in step 6—was to make sure the database contained the right keys, specifically PFAM, to proceed. Depending on the organism and database, the PFAM annotation may not exist. Here's how to check whether it does exist in the database you're interested in with two example databases, org.At.tair.db and org.Eck12.eg.db, an Arabidopsis database:
library(org.At.tair.db)columns(org.At.tair.db)
and an E.coli database:
library(org.EcK12.eg.db)columns(org.EcK12.eg.db)
Simply use the columns() function to report the data columns in the database. If PFAM shows up, you can follow the procedure. If it doesn't show up, then as an alternative procedure, it is possible to run PFAM ...
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