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

Description Constructor Author(s)


The parameters are used by the absoluteCN function.


GCAdjustParams(genome, mappability, min.mappability, n.bins = NULL, min.bin.size = 1, poly.degree = NULL, ploidy = 1) Creates a GCAdjustParams object.


A BSgenome object of the species that the experiment was done for.


A BSgenome object, 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.


Dario Strbenac

Search within the Repitools package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.