add_genesymbol {SWATH2stats} | R Documentation |
Gather gene symbols from biomart and add them to a data frame.
add_genesymbol( data_table, gene_ID_table, column_name = "Protein", ID1 = "uniprotswissprot", ID2 = "hgnc_symbol", id.separator = "/", copy_nonconverted = TRUE )
data_table |
A data frame or file name. |
gene_ID_table |
A table to match gene identifiers against |
column_name |
The column name where the original protein identifiers are present. |
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. |
Returns 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
{ gene_ID_table <- data.frame(uniprotswissprot = c("Q01581", "P49327", "P60709"), hgnc_symbol = c("HMGCS1", "FASN", "ACTB")) data_table <- data.frame(Protein = c("Q01581", "P49327", "2/P63261/P60709"), Abundance = c(100, 3390, 43423)) add_genesymbol(data_table, gene_ID_table) }