prepareData2 {EFMrep} | R Documentation |
Reorganasing data for calculation preparations per marker (simpler structure)
prepareData2(samples, refData = NULL, popFreq = NULL, minF = NULL, normalize = FALSE, AT = NULL, fillHomGen = TRUE, verbose = FALSE, doQ = TRUE)
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) |
Helpfunction to reorganising data for prepareC input Also takes detection thresholds as argument to remove possible alleles below the thresholds.
Restructured data in list used as input for functions evaluating the liklihood function
Oyvind Bleka