R Bioinformatics Cookbook

How to do it...

Finding protein domains with PFAM.db and bio3d can be done using the following steps:

1. Load the database package and inspect the types of keys in the database:

library(org.Hs.eg.db)keytypes(org.Hs.eg.db)

Note the ENSEMBL key in this output—we can use this to query the database.

2. Get a vector of keys using the keys() function:

k <- head(keys(org.Hs.eg.db, keytype = "ENSEMBL"), n = 3 )

3. Query the database:

result <- select(org.Hs.eg.db, keys = k, keytype="ENSEMBL", columns = c("PFAM"))result

4. Load the PFAM database to extract descriptions:

library(PFAM.db)
descriptions <- PFAMDE

5. Get all keys from the PFAM database:

all_ids <- mappedkeys(descriptions)

6. Get all descriptions for the PFAM IDs:

id_description_mapping <- as.data.frame(descriptions[all_ids]) ...