findGSEP (version 1.2.0)

findGSE_sp: Estimate Genome Size Using K-mer Frequencies

Description

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

Usage

findGSE_sp(
  histo = "",
  sizek = 0,
  outdir = "",
  exp_hom = 0,
  species = "",
  ploidy_ind = 2,
  avg_cov = 0,
  left_fit_ratio = 0.835,
  meanfit_old = 0,
  sdfit_old = 0,
  scale_flag = FALSE
)

Value

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

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.

ploidy_ind

An integer indicating the ploidy index (default is 2).

avg_cov

A numeric value representing the average coverage.

left_fit_ratio

A numeric value for the left fit ratio (default is 0.835).

meanfit_old

A numeric value representing the previous mean fit.

sdfit_old

A numeric value representing the previous standard deviation fit.

scale_flag

A logical value indicating whether to apply scaling (default is FALSE).

Examples

if (FALSE) {

histo <- "sample1.histo"
sizek <- 21
outdir <- tempdir()
exp_hom <- 200
species <- ""
ploidy_ind <- 2
avg_cov <- 0
left_fit_ratio <- 0.835
meanfit_old <- 0
sdfit_old <- 0
scale_flag <- FALSE
fit_lists <- findGSE_sp(path, samples, sizek, exp_hom, ploidy, range_left,
 range_right, xlimit, ylimit, output_dir)
}