add_genesymbol: Adds gene symbols to a table

In peterblattmann/SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

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)
  }

peterblattmann/SWATH2stats documentation built on July 2, 2023, 9:42 p.m.