run: Execution of SKIMA.

Description Usage Arguments Value Author(s) Examples

Description

Runs the SKIMA workflow.

Usage

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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")))

Arguments

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.

Value

None

Author(s)

Xavier Pastor x.pastorhostench@dkfz.de

Examples

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run()

xpastor/skima documentation built on May 16, 2019, 3:25 p.m.