findExcelGeneSymbols: Title function to identify Excel-mogrified gene symbols

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

Usage

findExcelGeneSymbols(x,
  mog.map = read.csv(system.file("extdata/mog_map.csv", package =
  "HGNChelper"), as.is = TRUE), regex = "impossibletomatch^")

Arguments

x	Vector of gene symbols to check for mogrified values
mog.map	Map of known mogrifications. This should be a dataframe with two columns: original and mogrified, containing the correct and incorrect symbols, respectively.
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.

Value

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.

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)

HGNChelper documentation built on Oct. 30, 2019, 9:41 a.m.