R/findExcelGeneSymbols.R

In waldronlab/HGNChelper: Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols

#' Title function to identify Excel-mogrified gene symbols
#' @description 
#' This function identifies gene symbols which may have been
#' mogrified by Excel or other spreadsheet programs.  If output is
#' assigned to a variable, it returns a vector of the same length
#' where symbols which could be mapped have been mapped.
#' @param x Vector of gene symbols to check for mogrified values
#' @param mog.map 
#'  Map of known mogrifications.  This should be
#'  a dataframe with two columns: original and mogrified, containing
#'  the correct and incorrect symbols, respectively.
#' @param regex 
#'  Regular expression, recognized by the base::grep function which
#'  is called with ignore.case=TRUE, to identify mogrified symbols.
#'  The default regex will not match anything. The regex in the
#'  examples is an attempt to match all Excel-mogrified HGNC human gene symbols.
#'  It is not necessary for all matches to have a corresponding entry
#'  in mog.map$mogrified; values in x which are matched by this regex
#'  but are not found in mog.map$mogrified simply will not be
#'  corrected. 
#' @return
#' if the return value of the function is assigned to a variable, the
#' function will return a vector of the same length as the input,
#' with corrections possible from mog.map made.
#' @export
#'
#' @examples
#' ## Available maps from this package:
#' human <- read.csv(system.file("extdata/mog_map.csv", 
#'                               package = "HGNChelper"), as.is=TRUE)
#' mouse <- read.csv(system.file("extdata/HGNChelper_mog_map_MGI_AMC_2016_03_30.csv", 
#'                               package = "HGNChelper"), as.is=TRUE)
#' ## This regex is based that provided by Zeeberg et al.,
#' ##  Mistaken Identifiers: Gene name errors can be introduced
#' ## inadvertently when using Excel in bioinformatics.  BMC
#' ##  Bioinformatics 2004, 5:80.
#' re <- "[0-9]\\-(JAN|FEB|MAR|APR|MAY|JUN|JUL|AUG|SEP|OCT|NOV|DEC)|[0-9]\\.[0-9][0-9]E\\+[[0-9][0-9]"
#' findExcelGeneSymbols(c("2-Apr", "APR2"), mog.map=human, regex=re)
#' findExcelGeneSymbols(c("1-Feb", "Feb1"), mog.map=mouse)
findExcelGeneSymbols <- function(x,
  mog.map=read.csv(system.file("extdata/mog_map.csv", package = "HGNChelper"), as.is=TRUE),
  regex="impossibletomatch^"
 ){
    if(class(x) != "character"){
        x <- as.character(x)
        warning("coercing x to character.")
    }
    if(!is(mog.map, "data.frame") || !identical(colnames(mog.map), c("original", "mogrified"))){
      stop("mog.map must be a data.frame with colnames 'original' and 'mogrified'")
    }
    mog.symbols <- grepl(pattern=regex, x, ignore.case=TRUE) | x %in% mog.map$mogrified
    mog.symbols <- x[mog.symbols]
    if(length(mog.symbols) > 0){
        mog.mapped <- data.frame(mogrified=mog.symbols,
                                 corrected=mog.map$original[ match(toupper(mog.symbols), toupper(mog.map$mogrified)) ],
                                 stringsAsFactors=FALSE)
        mog.mapped$abletofix <- ifelse(is.na(mog.mapped$corrected), "no", "yes")
        mog.mapped$corrected[is.na(mog.mapped$corrected)] <- mog.mapped$mogrified[is.na(mog.mapped$corrected)]
        warning.message <- paste(paste(mog.mapped$mogrified,
                                       mog.mapped$corrected,
                                       sep=" to "),
                                 collapse=", ")
        warning(paste("Transmogrified gene symbols found.  Returning the following corrections:", warning.message))
        mog.locations <- match(mog.mapped$mogrified, x)
        x[mog.locations] <- mog.mapped$corrected
    }
    return(x)
}