check_ID {canprot}R Documentation

Check UniProt IDs

Description

Do the IDs correspond to known UniProt IDs?

Usage

  check_ID(ID, aa_file = NULL, updates_file = NULL)

Arguments

ID

character or list, candidate UniProt IDs

aa_file

character, file name

updates_file

character, file name

Details

check_ID is used to check candidate IDs supplied in a character or list object. Multiple IDs can be separated by a semicolon. “Known” IDs are those that are present in the human_aa dataset of amino acid compositions.

If aa_file is specified, additional amino acid compositions to be considered are read from this file, which should be in the same format as e.g. human_extra.csv (see also thermo$protein). If updates_file is specified, these ID mappings are included alongside the packaged uniprot_updates.

Value

The function returns the IDs in a list (dropping the semicolons, but reflecting the original arrangement), replacing any unknown IDs with NA.

Examples

data(canprot)
# the function replaces the 3 non-existent IDs with NA
check_ID(c("P61247;PXXXXXX", "PYYYYYY;P46777;P60174", "PZZZZZZ"))

[Package canprot version 0.0.2 Index]