calculateKsDistribution4wgd_multiple: Calculate the Ks Distribution for Multiple Speices

In shinyWGD: 'Shiny' Application for Whole Genome Duplication Analysis

Calculate the Ks Distribution for Multiple Speices

Description

This function takes a list of data files, calculates the Ks distribution, and returns the results.

Usage

calculateKsDistribution4wgd_multiple(
  files_list,
  binWidth = 0.1,
  maxK = 5,
  plot.mode = "weighted",
  include.outliers = FALSE,
  minK = 0,
  minAlnLen = 0,
  minIdn = 0,
  minCov = 0
)

Arguments

files_list	A list of file paths containing Ks data.
binWidth	The width of Ks bins for the distribution.
maxK	The maximum Ks value to consider.
plot.mode	The mode for plotting ("weighted", "average", "min", or "pairwise").
include.outliers	Whether to include outliers in the calculation.
minK	The minimum Ks value to include in the distribution.
minAlnLen	The minimum alignment length to include in the distribution.
minIdn	The minimum alignment identity to include in the distribution.
minCov	The minimum alignment coverage to include in the distribution.

Value

A list containing two data frames: "bar" for Ks distribution and "density" for density data.

shinyWGD documentation built on April 4, 2025, 2:28 a.m.