This function identifies gene symbols which are outdated or may have been mogrified by Excel or other spreadsheet programs.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.
checkGeneSymbols(
x,
chromosome = NULL,
unmapped.as.na = TRUE,
map = NULL,
species = "human",
expand.ambiguous = FALSE
)A character vector of gene symbols to check for modified or outdated values
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.
If TRUE (default), unmapped symbols will appear as
NA in the Suggested.Symbol column. If FALSE, the original unmapped
symbol will be kept.
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.
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.
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.
The function will return a data.frame of the same number of rows as the input, with corrections possible from map.
mouse.table for the mouse lookup table, hgnc.table for the human lookup table
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: Mon Apr 4 17:31:23 2022
#> 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: Mon Apr 4 17:31:23 2022
#> 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: Mon Apr 4 17:31:23 2022
#> x Approved Suggested.Symbol
#> 1 AAVS1 TRUE AAVS1
checkGeneSymbols(human, expand.ambiguous=TRUE)
#> Maps last updated on: Mon Apr 4 17:31:23 2022
#> 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: Mon Apr 4 17:31:23 2022
#> x Approved Suggested.Symbol
#> 1 Cpamd8 TRUE Cpamd8
#> 2 Mug2 TRUE Mug2
checkGeneSymbols(mouse, species = "mouse", expand.ambiguous = TRUE)
#> Maps last updated on: Mon Apr 4 17:31:23 2022
#> 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)
}