read.wgd_ksd: Read the output file of wgd ksd

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

Read the output file of wgd ksd

Description

Read the output file of wgd ksd

Usage

read.wgd_ksd(
  file,
  include_outliers = FALSE,
  min_ks = 0,
  min_aln_len = 0,
  min_idn = 0,
  min_cov = 0
)

Arguments

file	The output file of ⁠wgd ksd⁠
include_outliers	Include outliers or not, default FALSE.
min_ks	Minimum Ks value, default 0.
min_aln_len	Minimum alignment length, default 0.
min_idn	Minimum alignment identity, default 0.
min_cov	Minimum alignment coverage, default 0.

Value

A ksv object, which is a list including:

• ks_df: the data frame that used for following analysis

• ks_dist: a list including a vector of Ks values in the distribution

• raw_df: raw data

• filters: filters that applied to the raw data

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