Indent code properly

[adeschen]

Indent code properly so it's easier to read/understand e.g.
runPermutationUsingMethylKitInfo(
samplesForTransgenerationalAnalysis,
type="sites", nbrPermutations=3, vSeed=221)
instead of
runPermutationUsingMethylKitInfo(methylKitInfo =
samplesForTransgenerationalAnalysis, type = "sites",
nbrPermutations = 3, vSeed = 221)