GCAdjustParams-class: Container for parameters for mappability and GC content...
In markrobinsonuzh/Repitools: Epigenomic tools
GCAdjustParams 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.
genomeA BSgenome object of the
species that the experiment was done for.
mappabilityA BSgenome object,
or the path to a FASTA file generated by
GEM mappability containing the mappability of
each base in the genome.
min.mappabilityA number between 0 and 100 that is a cutoff
on window mappability.
n.binsThe number of GC content bins to divide the windows
into, before finding the mode of counts in each window.
min.bin.sizeGC bins with less than this many count windows inside
them will be ignored.
poly.degreeThe degree of the polynomial to fit to the GC bins'
count modes.
ploidyA 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
markrobinsonuzh/Repitools documentation built on March 20, 2024, 6:04 a.m.
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| GCAdjustParams | 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.genomeA
BSgenomeobject of the species that the experiment was done for.mappabilityA
BSgenomeobject, or the path to a FASTA file generated by GEM mappability containing the mappability of each base in the genome.min.mappabilityA number between 0 and 100 that is a cutoff on window mappability.
n.binsThe number of GC content bins to divide the windows into, before finding the mode of counts in each window.
min.bin.sizeGC bins with less than this many count windows inside them will be ignored.
poly.degreeThe degree of the polynomial to fit to the GC bins' count modes.
ploidyA 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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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