Identify outdated or Excel-mogrified gene symbols

This function identifies gene symbols which are outdated or may have been mogrified by Excel or other spreadsheet programs.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A character vector of gene symbols to check for modified or outdated values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)
#> Maps last updated on: Sat Nov 16 10:35:32 2024
#> Warning: Human gene symbols should be all upper-case except for the 'orf' in open reading frames. The case of some letters was corrected.
#> Warning: x contains non-approved gene symbols
#>              x Approved   Suggested.Symbol
#> 1          FN1     TRUE                FN1
#> 2         TP53     TRUE               TP53
#> 3  UNKNOWNGENE    FALSE               <NA>
#> 4        7-Sep    FALSE            SEPTIN7
#> 5          9/7    FALSE            SEPTIN7
#> 6        1-Mar    FALSE MARCHF1 /// MTARC1
#> 7         Oct4    FALSE             POU5F1
#> 8        4-Oct    FALSE             POU5F1
#> 9     OCT4-PG4    FALSE           POU5F1P4
#> 10    C19ORF71    FALSE            TEKTIP1
#> 11    C19orf71    FALSE            TEKTIP1

## Mouse
mouse <- c("1-Feb", "Pzp", "A2m")
checkGeneSymbols(mouse, species="mouse")
#> Maps last updated on: Sat Nov 16 10:35:32 2024
#> Warning: x contains non-approved gene symbols
#>       x Approved Suggested.Symbol
#> 1 1-Feb    FALSE             Feb1
#> 2   Pzp     TRUE              Pzp
#> 3   A2m     TRUE              A2m

## expand.ambiguous

## Human
human <- "AAVS1"
checkGeneSymbols(human, expand.ambiguous=FALSE)
#> Maps last updated on: Sat Nov 16 10:35:32 2024
#>       x Approved Suggested.Symbol
#> 1 AAVS1     TRUE            AAVS1
checkGeneSymbols(human, expand.ambiguous=TRUE)
#> Maps last updated on: Sat Nov 16 10:35:32 2024
#>       x Approved   Suggested.Symbol
#> 1 AAVS1     TRUE AAVS1 /// PPP1R12C

## Mouse
mouse <- c("Cpamd8", "Mug2")
checkGeneSymbols(mouse, species = "mouse", expand.ambiguous = FALSE)
#> Maps last updated on: Sat Nov 16 10:35:32 2024
#>        x Approved Suggested.Symbol
#> 1 Cpamd8     TRUE           Cpamd8
#> 2   Mug2     TRUE             Mug2
checkGeneSymbols(mouse, species = "mouse", expand.ambiguous = TRUE)
#> Maps last updated on: Sat Nov 16 10:35:32 2024
#>        x Approved Suggested.Symbol
#> 1 Cpamd8     TRUE  Cpamd8 /// Mug2
#> 2   Mug2     TRUE  Mug2 /// Cpamd8

## 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)
}