GCAdjustParams-class: Container for parameters for mappability and GC content...

Description Constructor Author(s)

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.

Author(s)

Dario Strbenac


Repitools documentation built on Nov. 8, 2020, 7:52 p.m.