convert_protein_ids {SWATH2stats} | R Documentation

## 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.
`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.)
`host` | Path of the biomaRt database (e.g. "www.ensembl.org", "dec2017.archive.ensembl.org").
`mart` | The type of mart (e.g. "ENSEMBL_MART_ENSEMBL", etc.)
`ID1` | The type of the original protein identifiers (e.g. "uniprotswissprot", "ensembl_peptide_id").
`ID2` | The type of the converted protein identifiers (e.g. "hgnc_symbol", "mgi_symbol", "external_gene_name").
`id.separator` | Separator between protein identifiers of shared peptides.
`copy_nonconverted` | Option defining if the identifiers that cannot be converted should be copied.
`verbose` | Option to write a file containing the version of the database used.

### Value

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

     ## Not run:
      data_table <- data.frame(
           "Protein" = c("Q01581", "P49327", "2/P63261/P60709"),
           "Abundance" = c(100, 3390, 43423))
      convert_protein_ids(data_table)

    ## End(Not run)

[Package SWATH2stats version 1.24.0 Index]