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 1.14.0 Index]