prepareData2 {EFMrep}R Documentation

prepareData2

Description

Reorganasing data for calculation preparations per marker (simpler structure)

Usage

prepareData2(samples, refData = NULL, popFreq = NULL, minF = NULL,
  normalize = FALSE, AT = NULL, fillHomGen = TRUE, verbose = FALSE,
  doQ = TRUE)

Arguments

samples

A list with evidence profiles [[sample]][[locus]]$adata/hdata

refData

A list with reference profiles [[reference]][[locus]]$adata

popFreq

A list with population frequencies [[locus]]

minF

The freq value included for new alleles (new alleles as potential stutters will have 0). Default NULL is using min.observed in popFreq.

normalize

A boolean of whether normalization should be applied or not. Default is FALSE.

AT

A detection threshold value or thresholds per replicate or a list with per marker per replicate (marker names must be defined). NULL ignores filtering.

fillHomGen

A boolean of whether to fill in homozygote genotypes given with one allele

verbose

Whether to print out if new alleles are imputed

doQ

A boolean whether to Q-designate or not (i.e. whether non-observed alleles are grouped as Q-allele)

Details

Helpfunction to reorganising data for prepareC input Also takes detection thresholds as argument to remove possible alleles below the thresholds.

Value

Restructured data in list used as input for functions evaluating the liklihood function

Author(s)

Oyvind Bleka


[Package EFMrep version 1.0.0 Index]