findExcelGeneSymbols: function to identify Excel-mogrified gene symbols

In lwaldron/MistakenIdentities: Handy Functions for Working With HGNC Gene Symbols and Affymetrix Probeset Identifiers.

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. Note that this function is superceded by checkGeneSymbols, which corrects Excel-mogrified gene symbols as well as aliases and outdated symbols.

Usage

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

Arguments

x	Vector of gene symbols to check for mogrified values
mog.map	Map of known mogrifications. A default map is available with this package by data(mog.map), but any map may be used. 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. 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. 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.

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.

Author(s)

Levi Waldron and Markus Riester

See Also

checkGeneSymbols

lwaldron/MistakenIdentities documentation built on May 21, 2019, 9 a.m.