add_genesymbol {SWATH2stats} | R Documentation

## Adds gene symbols to a table

### Description

Gather gene symbols from biomart and add them to a data frame.

### Usage

    add_genesymbol(
      data_table,
      gene_ID_table,
      column_name = "Protein",
      ID1 = "uniprotswissprot",
      ID2 = "hgnc_symbol",
      id.separator = "/",
      copy_nonconverted = TRUE
    )

### Arguments

`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.

### 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

    {
      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)
      }

[Package SWATH2stats version 1.20.1 Index]