estimate_Genome_peakp: Function to fit 2p peak model, with p forms

In PauloMoraMartinez/Genomescope2.0_: Reference-free profiling of genomes

Function to fit 2p peak model, with p forms

Description

Function to fit 2p peak model, with p forms

Usage

estimate_Genome_peakp(kmer_hist_orig, x, y, k, p, topology, estKmercov,
  round, foldername, arguments)

Arguments

kmer_hist_orig	A data frame of the original histogram data (starting at 1 and with last position removed).
x	An integer vector of the x-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).
y	A numeric vector of the y-coordinates of the histogram (after filtering out low coverage errors and high coverage kmers).
k	An integer corresponding to the kmer length.
p	An integer corresponding to the ploidy.
topology	An integer corresponding to the topology to use.
estKmercov	An integer corresponding to the estimated kmer coverage of the polyploid genome. Set to -1 if not specified by user.
round	An integer corresponding to the iteration number (0, 1, 2, 3) for the fitting process.
foldername	A character vector corresponding to the name of the output directory.
arguments	A data frame of the user-specified inputs.

Value

A list (nls, nlsscore) where nls is the nlsLM model object (with some additional components) and nlsscore is the score (model RSSE) corresponding to the best fit (of the p forms).

PauloMoraMartinez/Genomescope2.0_ documentation built on April 5, 2022, 12:02 a.m.