genMPSevidence: genMPSevidence

In oyvble/MPSproto: A Quantitative Model for MPS data with complex stutters

genMPSevidence

Description

Function for generating replicated mixture samples given same contributors and model parameters.

Usage

genMPSevidence(
  calibration,
  NOC,
  popFreq,
  mu = 1000,
  omega = 0.1,
  beta = 1,
  sorted = FALSE,
  mx = NULL,
  refData = NULL,
  nrep = 1,
  kit = NULL,
  platform = "MPS"
)

Arguments

calibration	An object indicating the fitted calibration model (marker efficiency,stutters,noise) (MLE based)
NOC	Number of contributors
popFreq	A list of allele frequencies for a given population.
mu	Expected peak heights for a het. single contributor allele
omega	Coeffecient of variance of peak heights.
beta	Coeffecient related to degree of degradation.
sorted	Boolean for wheter sorting the contributors with respect to decreasingly mixture proportions.
mx	A vector of known mixture proportions. Default is random uniform.
refData	A list of given reference profiles given as refData[[i]][[s]]. Default is random from population.
nrep	Number of replicates (same contributors) to generate. Default is 1.
kit	Kitname for considered kit (shortname). Required for degradation model
platform	The platform name that is used

Details

genDataset samples random mixture peak heights given as gamma(rho*sum(h_k),tau), with h_k as peak height of k-te contributor. genData conditions on alleles given by refData. Empty references are generated with population frequencies.

Value

List with elements theta,samples,refData where theta is the true parameters of the model. samples is a list with samples which for each samples has locus-list elements with list elements adata and hdata

Author(s)

Oyvind Bleka

Examples

## Not run:  
kit = "ForenSeq"
pkg = path.package("MPSproto")
calib =  readRDS(paste0(pkg,"/paper_stutterChar/calibrated_MPSproto.RDS"))
popFreq =  importMPSfreqs(paste0(pkg,"/paper_stutterChar/freqFile_ForenSeqFWbrack_Norway.csv"))[[1]]
gen = genMPSevidence(calib,2,popFreq,mu=1000,omega=0.2,beta=1,kit=kit )
plotMPS(gen$samples,gen$refData,AT=10)

## End(Not run)

oyvble/MPSproto documentation built on March 19, 2024, 5:32 a.m.