pedigreesimR: PedigreeSim Management

In rramadeu/diaQTLSimulations: Simulate multi-population of polyploids for linkage analysis and QTL

Description

Wrap-up function to run PedigreeSim software, to simulate GBS data, and to do SNP calling with updog package

Usage

pedigreesimR(
  map,
  haplotypes,
  pedigree,
  centromere = NULL,
  prefPairing = 0,
  quadrivalents = 0,
  ploidy = 4,
  workingfolder = "PedigreeSimR_files",
  filename = "",
  mapfunction = "HALDANE",
  chromosome = "A",
  sampleHap = FALSE,
  seed = NULL,
  allownochiasmata = 1,
  naturalpairing = 0,
  parallelquadrivalents = 0,
  pairedcentromeres = 0,
  mapwidthpad = 4,
  epsilon = c(0, 0),
  missingFreq = c(0, 0),
  GBS = FALSE,
  GBSavgdepth = 60,
  GBSsnpcall = FALSE,
  GBSseq = 0.001,
  GBSbias = 0.7,
  GBSod = 0.005,
  GBSnc = 1,
  monoFilter = TRUE,
  trackErrorSim = FALSE,
  justEssential = FALSE
)

Arguments

map	vector of the marker position.
haplotypes	matrix with haplotype information to be draw
pedigree	pedigree data frame
centromere	numeric with its position
prefPairing	numeric
quadrivalents	numeric
ploidy	integer even number
workingfolder	string with folder name to write input/output files
filename	string with filename id to put in the beggining of the created files
mapfunction	"HALDANE" or "KOSAMBI"
chromosome	string
sampleHap	if TRUE sample haplotypes, if FALSE pick them in sequence
seed	integer to be used to sample haplotypes
allownochiasmata	numeric
naturalpairing	numeric
parallelquadrivalents	numeric
pairedcentromeres	numeric
mapwidthpad	numeric length of marker code
epsilon	vector with two epsilon values for error for genotypic assigment, vector with two values, the first is the parents' epsilon, the second is the offsprings
missingFreq	vector with two missingFreq values to sample missing values for the genotypes, the first is the parents' frequency, the second is the offsprings
GBS	if TRUE simulate GBS data and do SNP calling with updog
GBSavgdepth	average depth to sample total number of reads from Poisson distribution
GBSsnpcall	if TRUE performs SNP calling using updog
GBSseq	the sequencing error rate (rflexdog inner function)
GBSbias	the bias parameter Pr(a read after selected) / Pr(A read after selected) (rflexdog inner function). (rflexdog inner function)
GBSod	the overdispersion parameter (rflexdog inner function).
GBSnc	number of cores for the parallelization for SNP calling
monoFilter	if TRUE filter monomorphic markers from haplotypes
trackErrorSim	if TRUE create a spreadsheet with the simulate error positions given epsilon and missingData (1 if error, 0 if not)
justEssential	it will just run the simulation and avoid GBS/Dosage Calling/Parental haplotype

Value

nothing

Author(s)

Rodrigo R Amadeu, [e-mail]

Examples

## Not run: 
map = 1:100
haplotypes = fake_haplo(m=50,n=100,seed=1234)
pedigree = diallel_pedigree(parents=7,popsize=1000,selfs=2)
pedigreesimR(map,haplotypes,pedigree)

## End(Not run)

rramadeu/diaQTLSimulations documentation built on Feb. 11, 2022, 1:34 a.m.