add_genesymbol: Adds gene symbols to a table
In SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

Description Usage Arguments Value Note Author(s) Examples

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)
  }