Summarize.LOD: Summarize the LOD scores from parentage inference with FRANz

In patbarry6/PseudoBabies: Assess power of genetic markers for parentage through simulation

Description

This function summarizes the LOD scores from parentage inference of PseudoBabies simulations with the software FRANz.

Usage

Summarize.LOD(
  AnalysisName,
  nSim,
  Miss_data = FALSE,
  MissingVec = c(0, 2.5),
  Geno_Error = FALSE,
  ErrorVec = c(0, 2),
  SavePlot = FALSE,
  PlotName = "LODsum",
  Plots = c("LCA", "PLCA", "PLCA", "PLICA"),
  ErrorLab,
  Markerfile,
  ...
)

Arguments

AnalysisName	Name of the Analysis
Miss_data	Would you like to add missing data to the simulations? Defaults to FALSE
MissingVec	A vector of values for the percent of missing data in the input file. Required if Miss_data=TRUE. Defaults to 0 and 2.5 percent.
Geno_Error	Would you like to add genotyping error to the simualated data? Defaults to FALSE
ErrorVec	A vector of error values for genotyping error. Required if Geno_Error=TRUE. Defaults to 0 and 2 percent.
SavePlot	Do you want to create plots? Defaults to FALSE
PlotName	What do you want to name your plots? Defaults to LODsum
Plots	What plots do you want to create? Options are 'LCA','PLCA','PLCA','PLICA'.
ErrorLab	Label for Error in plots
Markerfile	.csv for marker panels that will be evaluated.
nSims	Number of replicate simulations

Examples

summarize.LOD()

patbarry6/PseudoBabies documentation built on Dec. 22, 2021, 6:41 a.m.