prepareData: prepareData

In oyvble/euroformix: A Quantitative Model for Interpreting DNA Mixtures

prepareData

Description

Reorganasing data for calculation preparations

Usage

prepareData(
  mixData,
  refData = NULL,
  popFreq = NULL,
  minF = NULL,
  normalize = FALSE,
  threshT = NULL,
  fillHomGen = TRUE,
  verbose = TRUE
)

Arguments

mixData	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	Whether normalization should be applied or not. Default is FALSE.
threshT	A detection threshold value or thresholds per makers (marker names must be defined). NULL ignores filtering.
fillHomGen	Whether to fill in homozygote genotypes given with one allele
verbose	Whether printing out information

Details

Optionally to use beforehand (still required for Qual. calcs) Helpfunction to reorganising data which are input for further calculations (includes Qassignation). 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

oyvble/euroformix documentation built on Aug. 25, 2023, 11:14 a.m.