Simulate median allele ratios for varying number of samples and depth values

This function will simulate the expected median allele ratios under HWE for given ranges of no. of samples and depth coverage values. This is useful if you need to find the cutoff values of allele ratios for different no. of samples and depth of coverage values in your data set.

Usage

depthVsSample(
  cov.len = 100,
  sam.len = 100,
  nsims = 1000,
  plot = TRUE,
  col = c("#1C86EE", "#00BFFF", "#DAA520", "#FF0000")
)

Arguments

cov.len

max value of depth of coverage to be simulated

sam.len

maximum no. of samples to be simulated

nsims

numerical. no. of simulations to be done for each combination of samples and depth depth and no. samples ranges

plot

logical. Whether to plot the output (a plot of no. samples vs median depth of coverage colored by median allele ratios)

col

character. Two colors to add to the gradient

Value

A matrix of median allele ratios where rows are the number of samples and columns are depth of coverage values

Author

Pascal Milesi, Piyal Karunarathne

Examples

if (FALSE) depthVsSample(cov.len=100,sam.len=100)