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