findGSE_raw: Estimate Genome Size Using Raw K-mer Frequencies

In findGSEP: Estimate Genome Size of Polyploid Species Using k-Mer Frequencies

Estimate Genome Size Using Raw K-mer Frequencies

Description

This function estimates the genome size of a species using raw k-mer frequencies.

Usage

findGSE_raw(histo = "", sizek = 0, outdir = "", exp_hom = 0, species = "")

Arguments

histo	A character string specifying the path to the histogram file.
sizek	An integer indicating the size of k used to generate the histogram.
outdir	A character string specifying the output directory. If not specify, will use tempdir() as output directory.
exp_hom	A numeric value representing the expected average k-mer coverage for the homozygous regions.
species	A character string specifying the species name.

Value

A list containing the estimated genome size and other fitting parameters.

Examples

## Not run: 

histo <- "sample1.histo"
sizek <- 21
outdir <- tempdir()
exp_hom <- 200
species <- ""
fit_lists <- findGSE_raw(histo, sizek,output_dir, exp_hom, species)

## End(Not run)

findGSEP documentation built on May 29, 2024, 3:35 a.m.