start_wash_cycle: function begins the online rPCA process. Use this function if...
In kcygan/dryclean: rPCA based method to de-noise genomic coverage data

Description Usage Arguments Value Author(s)

function begins the online rPCA process. It is the wrapper that takes in GRanges and outputs GRanges with decomposition

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start_wash_cycle(cov, mc.cores = 1, detergent.pon.path = NA,
  verbose = TRUE, whole_genome = TRUE, use.blacklist = FALSE,
  chr = NA, germline.filter = TRUE, germline.file = NA)

`cov`	GRanges object containig the GC corrected cov data outputed from fragCounter. Needs metadata with header "reads.corrected".
`mc.cores`	interger (default == 1). Number of cores to use for parallelization.
`detergent.pon.path`	string. Path to pon/detergent genrated using normal samples.
`verbose`	boolean (default == TRUE). Outputs progress.
`whole_genome`	boolean (default = TRUE). For this function always set this parameter to TRUE.
`use.blacklist`	boolean (default = FALSE). Whether to exclude off-target markers in case of Exomes or targeted sequqnecing. If set to TRUE, needs a GRange marking if each marker is set to be excluded or not.
`chr`	integer (default == NA). Depricated. Can be used to decompose a single chromosome.
`germline.filter`	boolean (default == TRUE). If germline markers need to be removed from decomposition.
`germline.file`	character (default == NA). Path to file with germline markers.