remap_accessions: Remap accessions

In vladpetyuk/PlexedPiper: Pipeline for isobaric quantification.

Description

Converting accessions from RefSeq to Gene. If 'conversion_table' is not supplied, the function leverages 'AnnotationHub()'

Usage

remap_accessions_refseq_to_gene(msnid, organism_name, conversion_table)

remap_accessions_uniprot_to_gene(msnid, organism_name, conversion_table)

Arguments

msnid	(MSnID object) MS/MS ID data
organism_name	(string) Official organism name
conversion_table	(data.frame) data frame with two columns one should with named accessions and contain accessions from 'msnid' object (e.g. RefSeq) the other is with alternative annotation to map to (e.g. gene symbol).

Value

(MSnID object) MS/MS ID data with computed number of peptides per 1000 aa. Added column name - "peptides_per_1000aa".

Examples

path_to_MSGF_results <- system.file("extdata/global/msgf_output", package = "PlexedPiperTestData")
msnid <- read_msgf_data(path_to_MSGF_results)
show(msnid)
msnid <- remap_accessions_refseq_to_gene(msnid, organism_name="Rattus norvegicus")
show(msnid)

vladpetyuk/PlexedPiper documentation built on June 24, 2021, 8:59 a.m.