solution_accuracy.pipeline: At each position, plot the pileup frequency for a given...

In SLeviyang/RegressHaplo: Haplotype Reconstruction Using Penalized Regression

At each position, plot the pileup frequency for a given nucleotide against the predicted frequency based on the RegressHaplo solution

Description

At each position, plot the pileup frequency for a given nucleotide against the predicted frequency based on the RegressHaplo solution

Usage

solution_accuracy.pipeline(
  out_dir,
  solution,
  nucs = c("A", "C", "G", "T"),
  variable_positions = NULL,
  plot = T
)

Arguments

out_dir	output directory with RegressHaplo files
solution	solution number
variable_positions	a numeric vector giving the variable positions to include. If NULL, then all variable positions are included (returned by get_variable_positions.pipeline)
plot	should the frequencies be plotted?
nuc	which nucleotide shoud be analyzed, one of "A", "C", "G", "T", "d", "i"

Value

a data.frame giving the true and predicted frequency at each position, nucleotide combination and a ggplot object of the frequencies

SLeviyang/RegressHaplo documentation built on June 1, 2022, 10:48 p.m.