Converting accessions from RefSeq to Gene. If conversion_table is not
supplied, the function leverages fetch_conversion_table.
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
(character) Scientific name of organism.
- conversion_table
(data.frame) Optional data.frame with two columns. One column should match the accessions from the `msnid` object (e.g. RefSeq). The other column is for the alternate 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
if (FALSE) {
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)
}