convert_protein_ids: Convert protein ids

In SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

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)

SWATH2stats documentation built on April 17, 2021, 6:01 p.m.