GCAdjustParams {Repitools} | R Documentation

## 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.

### Author(s)

Dario Strbenac

[Package Repitools version 1.32.0 Index]