Return a data.frame of AssayData name substitutions

The Illumina methylation platforms use two distinct technologies, the "goldengate" platform and the "infinium" platform. Each uses different file formats as well as different assay chemistry. To make the downstream data handling more straightforward and uniform between the two, a simple mapping from the column names in the output files of the Illumina software converts Red/Green or Cy5/Cy3 to unmethylated/methylated. This function returns that mapping.

Usage

getAssayDataNameSubstitutions()

Value

A data.frame with two columns, regex and replacement.

Details

A file in the `extdata` directory called `substitutions.txt` contains two columns. The function loads this file and uses the first column as a match against column names in the data file (with the "sample part" removed). If matched, the second column gives the replacement.

Author

Sean Davis <seandavi@gmail.com>

Examples

getAssayDataNameSubstitutions()
#>            regex       result
#> 1       AVG_Beta        betas
#> 2 Detection Pval        pvals
#> 3     Signal CY3 unmethylated
#> 4     Signal CY5   methylated
#> 5     Signal_Red unmethylated
#> 6     Signal_Grn   methylated
#> 7       Signal_A unmethylated
#> 8       Signal_B   methylated