Container for parameters for mappability and GC content adjusted absolute copy number estimation.
The parameters are used by the
GCAdjustParams(genome, mappability, min.mappability, n.bins = NULL, min.bin.size = 1, poly.degree = NULL, ploidy = 1)Creates a GCAdjustParams object.
BSgenomeobject of the species that the experiment was done for.
BSgenomeobject, or the path to a FASTA file generated by GEM mappability containing the mappability of each base in the genome.
A number between 0 and 100 that is a cutoff on window mappability.
The number of GC content bins to divide the windows into, before finding the mode of counts in each window.
GC bins with less than this many count windows inside them will be ignored.
The degree of the polynomial to fit to the GC bins' count modes.
A vector of multipliers to use on the estimated absolute copy number of each sample, if the number of sets of chromosomes is known.