add_genesymbol {SWATH2stats} | R Documentation

## add_genesymbol: Adds gene symbols to a table

### Description

This function adds an additional gene or protein symbol to a table.

### 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 dictionary table containing the original and new identifiers.
`column.name` | The column name where the original protein identifiers are present.
`ID1` | The type of the original protein identifiers.
`ID2` | The type of the converted protein identifiers.
`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.

### 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 1.18.0 Index]