HGNChelper (version 0.3.4)

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 Note that this function is superceded by checkGeneSymbols, which corrects Excel-mogrified gene symbols as well as aliases and outdated symbols.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

function will return a vector of the same length as the input, with corrections possible from mog.map made.

See Also

checkGeneSymbols