checkGeneSymbols: function to identify outdated or Excel-mogrified gene symbols

In lwaldron/MistakenIdentities: Handy Functions for Working With HGNC Gene Symbols and Affymetrix Probeset Identifiers.

Description

This function identifies gene symbols which are outdated or may have been mogrified by Excel or other spreadsheet programs. If output is assigned to a variable, it returns a data.frame of the same number of rows as the input, with a second column indicating whether the symbols are valid and a third column with a corrected gene list.

Usage

checkGeneSymbols(x, unmapped.as.na=TRUE, hgnc.table=NULL)

Arguments

x	Vector of gene symbols to check for mogrified or outdated values
unmapped.as.na	If TRUE, unmapped symbols will appear as NA in the Suggested.Symbol column. If FALSE, the original unmapped symbol will be kept when no correction can be found.
hgnc.table	If hgnc.table is a data.frame with colnames(hgnc.table) identical to c("Symbol", "Approved.Symbol"), it is used to correct gene symbols in x. Otherwise, the default table data("hgnc.table", package="HGNChelper") is used. The function used for creating this the hgnc.table dataframe can be found in the inst/hgncLookup.R file, in the source of this package. By default the hgnc.table dataframe shipped with this package is used (see ?hgnc.table)

Value

The function will return a data.frame of the same number of rows as the input, with corrections possible from hgnc.table.

Author(s)

Levi Waldron and Markus Riester

See Also

hgnc.table

Examples

library(HGNChelper)

x = c("FN1", "TP53", "UNKNOWNGENE","7-Sep", "9/7", "1-Mar", "Oct4", "4-Oct",
      "OCT4-PG4", "C19ORF71", "C19orf71")

res <- checkGeneSymbols(x)
res

if (interactive()){
    ##Run checkGeneSymbols with a brand-new map downloaded from HGNC:
    source(system.file("hgncLookup.R", package = "HGNChelper"))
    ##You should save this if you are going to use it multiple times,
    ##then load it from file rather than burdening HGNC's servers.
    ## save(hgnc.table, file="hgnc.table.rda", compress="bzip2")
    ## load("hgnc.table.rda")
    res <- checkGeneSymbols(x, hgnc.table=hgnc.table)
}

lwaldron/MistakenIdentities documentation built on May 21, 2019, 9 a.m.