convert_protein_ids {SWATH2stats} | R Documentation |
This function renames protein ids in a data frame or file
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 )
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. |
The data frame with an added column of the converted protein identifiers.
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")
Peter Blattmann
## 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)