convert_protein_ids {SWATH2stats} | R Documentation

## convert_protein_ids: Convert protein ids

### Description

This function renames protein ids in a data frame or file

### Usage

    convert_protein_ids(data_table,
                     column.name = "Protein",
                     species = "hsapiens_gene_ensembl",
                     host = "www.ensembl.org",
                     mart = "ENSEMBL_MART_ENSEMBL",
                     ID1 = "uniprotswissprot",
                     ID2 = "hgnc_symbol",
                     id.separator = "/",
                     copy_nonconverted = TRUE,
                     verbose = FALSE)

### Arguments

`data_table` | A data frame or file name.
`column.name` | The column name where the original protein identifiers are present. Default: "Protein".
`species` | The species of the protein identifiers in the term used by biomaRt (e.g. "hsapiens_gene_ensembl", "mmusculus_gene_ensembl", "drerio_gene_ensembl", etc.). Default: "hsapiens_gene_ensembl".
`host` | Path of the biomaRt database (e.g. "www.ensembl.org", "dec2017.archive.ensembl.org"). Default: "www.ensembl.org".
`mart` | The type of mart (e.g. "ENSEMBL_MART_ENSEMBL", etc.). Default: "ENSEMBL_MART_ENSEMBL"
`ID1` | The type of the original protein identifiers (e.g. "uniprotswissprot", "ensembl_peptide_id"). Default: "uniprotswissprot".
`ID2` | The type of the converted protein identifiers (e.g. "hgnc_symbol", "mgi_symbol", "external_gene_name"). Default: "hgnc_symbol".
`id.separator` | Separator between protein identifiers of shared peptides. Default: "/".
`copy_nonconverted` | Option defining if the identifiers that cannot be converted should be copied. Default: TRUE.
`verbose` | Option to write a file containing the version of the database used. Default: FALSE.

### Value

Returns the data frame with an added column of the converted protein identifiers.

### Note

Protein identifiers from shared peptides should be separated by a forward slash. The host of archived ensembl databases can be introduced as well (e.g. "dec2017.archive.ensembl.org")

### Author(s)

Peter Blattmann

### Examples

    data_table <- data.frame(Protein = c("Q01581", "P49327", "2/P63261/P60709"),
    Abundance = c(100, 3390, 43423))
    convert_protein_ids(data_table)

[Package SWATH2stats version 1.18.0 Index]