id_is_present: Checks if protein id appears in the headers of a fasta file.

In compomics/search-all-assess-subset: An implementation of the Search All, Asses Subset strategy for FDR estimation shotgun proteomics.

Description

Checks if protein id appears in the headers of a fasta file.

Usage

id_is_present(protein_id, fastapath)

Arguments

protein_id	Vector of protein ids.
fastapath	Location of the fasta file.

Value

Logical vector, TRUE if protein id is present in provided fasta file, FALSE otherwise.

Examples

## Location of the zipped data files
zip_file_path = system.file("extdata", "extdata.zip", package = "saas")

## Unzip and get the (temporary) location of the mzid file with the MS-GF+ search results from a
## competitive target decoy search of the complete pyrococcus proteome against a pyrococcus dataset.
mzid_file_path = unzip(zip_file_path, 'pyrococcus.mzid',exdir = tempdir())
## Read and parse the mzid file
dat = parse_msgf_mzid(mzid_file_path)

## Unzip and get the (temporary) location of the file with fasta headers.
## Each fasta header contains a protein_id from the protein subset of interest.
## These protein_ids match the protein_ids in the mzid result file.
fasta_file_path = unzip(zip_file_path, 'transferase_activity_[GO:0016740].fasta', exdir = tempdir())
protein_ids = unique(dat$protein_id)
head(protein_ids)
is_subset = id_is_present(protein_ids, fasta_file_path)
## Check how many of the identified proteins are subset and non subset protiens.
table(is_subset)

compomics/search-all-assess-subset documentation built on May 13, 2019, 9:55 p.m.