The R script for bioinformatic and statistical analyses of data obtained from Infinium MethylationEPIC microarray.
The arguments should be placed in the following order:
1 - a directory where microarray data are stored,
2 - a csv file with microarray data description,
3 - a directory where the analysis results should be saved,
4 - a Boolean value (TRUE/FALSE) determining if the data binarization step should be performed,
5 - a number of CPU threads to be used,
6 - a variable in the aforementioned csv file containing sample names,
7 - a variable in the aforementioned csv file containing sample sources,
8 - a variable in the aforementioned csv file containing sample genders,
9 - a variable in the aforementioned csv file containing sample descriptions,
10 - independent factor variables in the aforementioned csv file to be used, separated with '+', starting with a main categorical variable,
11 - a variable containing the Sentrix IDs,
12 - a variable containing the Sentrix Positions,
13 - a path to the optional txt file containing the list of CpG sites (one per a line) for which the methylation status visualization is to be performed (NA if none).