identify_germline: This is first phase in preparing the Panel of Normals (PON)...
In kcygan/dryclean: rPCA based method to de-noise genomic coverage data

Description Usage Arguments Value Author(s)

This function takes in gRanges outputs from fragCounter and extracts GC corrected read count data and carries rPCA decomposition on the matrix thus created

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identify_germline(normal.table.path = NA, signal.thresh = 0.5,
  pct.thresh = 0.98, verbose = TRUE, save.grm = FALSE,
  path.to.save = NA, num.cores = 1)

`normal.table.path`	character path to data.table containing two columns "sample", "normal_cov" and additional column "decomposed_cov" that contains drycleaned normal sample outputs. See manual for details.
`signal.thresh`	numeric (default == 0.5). This is the threshold to be used to identify an amplification (markers with signal intensity > 0.5) or deletions (markers with signal intensity < -0.5) in log space from dryclean outputs.
`pct.thresh`	numeric (default == 0.98). Proportion of samples in which a given marker is free of germline event.
`verbose`	boolean (default == TRUE). Outputs progress.
`save.grm`	boolean (default == FALSE). If the germline list needs to be saved.
`path.to.save`	charater (default == NA). Path to save the germline list created if save.grm == TRUE.
`num.cores`	interger (default == 1). Number of cores to use for parallelization.