error_minimize3: Minimize the Error for Remaining K-mer Frequency

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

Minimize the Error for Remaining K-mer Frequency

Description

This function minimizes the error for the remaining k-mer frequency by adjusting the scaling factor.

Usage

error_minimize3(
  tooptimize,
  x,
  end,
  xfit_left,
  xfit_right,
  d,
  min_valid_pos,
  itr,
  meanfit,
  sdfit
)

Arguments

tooptimize	A numeric vector containing the scale factors to optimize.
x	A numeric vector representing the histogram.
end	An integer indicating the right-side position for fitting.
xfit_left	A numeric value for the left-side position to calculate initial mean and standard deviation.
xfit_right	A numeric value for the right-side position to calculate initial mean and standard deviation.
d	A data frame representing the observed k-mer frequencies that will be fitted.
min_valid_pos	An integer indicating the left-side position from which the observed k-mer frequencies will be fitted.
itr	An integer representing the iteration count.
meanfit	A numeric value representing the initial mean.
sdfit	A numeric value representing the initial standard deviation.

Value

A numeric value representing the minimized error.

Examples

tooptimize <- c(1, 1, 1, 1)
x <- rnorm(100)
end <- 100
xfit <- seq(min(x), max(x), length=end)
xfit_left <- 20
xfit_right <- 80
d <- data.frame(V1=1:100, V2=rnorm(100))
min_valid_pos <- 10
itr <- 100
meanfit <- 18
sdfit <- 4.21
error <- error_minimize3(tooptimize, x, end, xfit_left, xfit_right, d,
min_valid_pos, itr, meanfit, sdfit)
print(error)

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