checkSYMBOLS: Checks Gene Symbol Validity
In renozao/xbioc: Extra Base Functions for Bioconductor

Description Usage Arguments Details Value References Examples

Look for gene symbols that were transformed by Excel nasty default setting, which interpreted them as dates or numeric.

1	checkSYMBOLS(x, value = FALSE, replace = FALSE, quiet = TRUE)

`x`	Character vector of gene symbols to check
`value`	Logical that indicates if the value of invalid symbols should be returned (`TRUE`), or only their index (`FALSE`).
`replace`	logical that indicates if fixable symbols should be replaced with their correct value. If `value = FALSE`, then the corrected symbols are set as names of the result integer vector, and the incorrect (input) symbols as values. If `value = FALSE`, then the corrected symbols are returned as values of the result character vector, and the incorrect (input) symbols as names.

This issue, although well known in the bioinformatics community, regularly surfaces to the detriment of the person who analyses the data. It has been reported to affect several publications and even large genomic projects (Zeeberg et al. (2004); Ziemann et al. (2016), Zeeberg et al. (2004); Ziemann et al. (2016)).

character or integer vector depending on the value of argument value. See help for argument replace, as this affects what goes into names and values of the result vector.

Zeeberg BR, Riss J, Kane DW, Bussey KJ, Uchio E, Linehan WM, Barrett JC, Weinstein JN (2004). "No Title." _BMC Bioinformatics_, *5*(1), 80. ISSN 14712105, doi: 10.1186/1471-2105-5-80 (URL: https://doi.org/10.1186/1471-2105-5-80).

Ziemann M, Eren Y, El-osta A (2016). "Gene name errors are widespread in the scientific literature." _Genome Biology_, 17-19. ISSN 1474-760X, doi: 10.1186/s13059-016-1044-7 (URL: https://doi.org/10.1186/s13059-016-1044-7).

bad_symbols <- c('AAA', 'BBB', '1-Dec', '10-JAN')
# index of incorrect symbols
checkSYMBOLS(bad_symbols)
# incorrect symbols
checkSYMBOLS(bad_symbols, value = TRUE)
# return fixed symbols as names (index vector)
checkSYMBOLS(bad_symbols, replace = TRUE)
# return fixed symbols as values (mapping)
checkSYMBOLS(bad_symbols, value = TRUE, replace = TRUE)