remap_accessions {MSnID} | R Documentation

## Changes accessions from one protein id to another

### Description

Changes accessions from one protein id to another.

### Usage

        remap_accessions(object,
                         conversion_table,
                         extraction_pttrn=c("\\|([^|-]+)(-\\d+)?\\|",
                                            "([A-Z]P_\\d+)",
                                            "(ENS[A-Z0-9]+)"),
                         path_to_FASTA=NULL)

### Arguments

`object` | An instance of class "MSnID".
`conversion_table` | (data.frame) first column in the data frame corresponds to identifiers in the FASTA file. Second column is the new identifier.
`extraction_pttrn` | (string) regex pattern that extract protein identifier from FASTA entry name as first group (that is `"\\1"`). The most common patterns are the one corresponding to UniProt `"\\|([^|-]+)(-\\d+)?\\|"`, RefSeq `"^([A-Z]P_\\d+)"` and ENSEMBL `"^(ENS[A-Z0-9]+)"`. Other regex patterns can be accepted as well. Defaul is UniProt pattern.
`path_to_FASTA` | (string) path to FASTA file. If provided only accessions present in the given FASTA file will be retained.

### Value

Returns an instance of "MSnID" with updated `accessions`.

### Author(s)

Vladislav A Petyuk vladislav.petyuk@pnnl.gov

### See Also

`remap_fasta_entry_names`

### Examples

    m <- MSnID(".")
    mzids <- system.file("extdata","phospho.mzid.gz",package="MSnID")
    m <- read_mzIDs(m, mzids)
    head(m$accessions)
    conv_tab <- fetch_conversion_table("Homo sapiens", "UNIPROT", "SYMBOL")
    m2 <- remap_accessions(m, conv_tab, "\\|([^|-]+)(-\\d+)?\\|")
    head(m2$accessions)
    unlink(".Rcache", recursive=TRUE)

[Package MSnID version 1.28.0 Index]