score_model: Score nlsLM model by number and percent of residual errors...

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

Score nlsLM model by number and percent of residual errors after excluding sequencing errors

Description

Score nlsLM model by number and percent of residual errors after excluding sequencing errors

Usage

score_model(kmer_hist_orig, nls, round, foldername)

Arguments

kmer_hist_orig	A data frame of the original histogram data (starting at 1 and with last position removed).
nls	An nlsLM model object.
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.

Value

A data frame where the variables "all", "full", and "unique" correspond to the model residual sum of square error (excluding sequencing error) including x-values up to the end of kmer_hist_orig, up to (2p+1)*lambda, and up to (p+1)*lambda respectively. Additionally, the variables "allscore", "fullscore", and "uniquescore" are the corresponding percentage of kmers that are correctly modeled.

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