checkGeneSymbols {HGNChelper}

Identify outdated or Excel-mogrified gene symbols

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This function identifies gene symbols which are outdated or may have been mogrified by Excel or other spreadsheet programs.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,
  chromosome = NULL,
  unmapped.as.na = TRUE,
  map = NULL,
  species = "human",
  expand.ambiguous = FALSE
)

Arguments

x

A character vector of gene symbols to check for modified or outdated values

chromosome

An optional integer vector containing the chromosome number of each gene provided through the argument x. It should be the same length as the input for x. Currently, this argument is implemented only for human gene cases.

unmapped.as.na

If TRUE (default), unmapped symbols will appear as NA in the Suggested.Symbol column. If FALSE, the original unmapped symbol will be kept.

map

Specify if you do not want to use the default maps provided by setting species equal to "mouse" or "human". Map can be any other data.frame with colnames identical to c("Symbol", "Approved.Symbol"). The default maps can be updated by running the interactive example below.

species

A character vector of length 1, either "human" (default) or "mouse". If NULL, or anything other than "human" or "mouse", then the map argument must be provided.

expand.ambiguous

If FALSE (default), genes with multiple mapping will only map to its approved symbol as the correct one. If TRUE, genes with multiple/ambiguous mapping will map to all the symbols linked to it.

Value

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

See Also

mouse.table for the mouse lookup table, hgnc.table for the human lookup table

Examples

library(HGNChelper)

## Human
human <- c("FN1", "TP53", "UNKNOWNGENE","7-Sep", "9/7", "1-Mar", "Oct4", "4-Oct",
      "OCT4-PG4", "C19ORF71", "C19orf71")
checkGeneSymbols(human)

## Mouse
mouse <- c("1-Feb", "Pzp", "A2m")
checkGeneSymbols(mouse, species="mouse")

## expand.ambiguous

## Human
human <- "AAVS1"
checkGeneSymbols(human, expand.ambiguous=FALSE)
checkGeneSymbols(human, expand.ambiguous=TRUE)

## Mouse
mouse <- c("Cpamd8", "Mug2")
checkGeneSymbols(mouse, species = "mouse", expand.ambiguous = FALSE)
checkGeneSymbols(mouse, species = "mouse", expand.ambiguous = TRUE)

## Updating the map
if (interactive()) {
    currentHumanMap <- getCurrentHumanMap()
    checkGeneSymbols(human, map=currentHumanMap)

    # 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")
    checkGeneSymbols(human, map=hgnc.table)
}