run: Execution of SKIMA.
In xpastor/skima:

Description Usage Arguments Value Author(s) Examples

Runs the SKIMA workflow.

run(idat_dir = Sys.getenv("IDAT_DIR"),
  sample.annotation = Sys.getenv("SAMPLE_ANNOTATION"),
  blacklist = Sys.getenv("BLACKLIST"), outdir = Sys.getenv("OUTDIR"),
  runCNV = as.logical(Sys.getenv("RUN_CNV")),
  diffMeth = as.logical(Sys.getenv("RUN_DIFFERENTIAL_METHYLATION")),
  removeSNPs = as.logical(Sys.getenv("REMOVE_SNPS")),
  population = Sys.getenv("POPULATION"),
  usePredictedSex = as.logical(Sys.getenv("USE_PREDICTED_SEX")),
  batch.vars = Sys.getenv("BATCH_VARS"),
  seed = as.integer(Sys.getenv("SEED")),
  ncores = as.integer(Sys.getenv("NCORES")))

`idat_dir`	character. Path to the directory with the idat files.
`sample.annotation`	character. Path to the sample sheet with all the annotation about the samples. Must have a column named 'Sample_Name' with unique sample identifiers, a column named 'Sentrix_ID' with the array identifier and a column named 'Sentrix_Position' with the position in the array where the sample was hybridized.
`blacklist`	character. Path to a file with probes to be flagged or removed from the analysis.
`outdir`	character. Directory where all the results will be writen.
`runCNV`	boolean. Should the CNV analysis be run?
`diffMeth`	boolean. Should the differential methylation analsysis be run?
`removeSNPs`	boolean. Should polymorphic probes with an allellic frequency higher than 1/nrow(sample.annotation) in the population given in 'population' be removed?
`population`	character. A string defining the population where to compare allellic frequencies. One of: NULL, ”, 'AFR', 'AMR', 'ASN', 'EUR', 'SAS', 'EAS'. NULL and ” will compare to global allellic frequencies.
`usePredictedSex`	boolean. Should the predicted sex be included in the analysis, and used as confounding variable?
`batch.vars`	character. String with a list of columns from `'sample.annotation'` separated by comas to be used as confounding variables.
`seed`	integer. Seed to avoid randomness and make the analysis reproducible.
`ncores`	integer. Number of cores to use for the multithreaded processes.