simulateGenos: Simulate recombination events in R

Description Usage Arguments

Description

This function simulates genotypes within a pedigree, based on centiMorgan map distances. Outputs genotypes as a GenABEL gwaa object.

Usage

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simulateGenos(ped, pedigree.type = "simple", cM = NULL, cM.male = NULL,
  cM.female = NULL, founder.mafs = NULL, chromosome.ids = NULL,
  snp.names = NULL, map.distances = NULL, error.rate = 1e-04,
  missing.rate = 0.001, xover.min.cM = NULL, xover.min.cM.male = NULL,
  xover.min.cM.female = NULL)

Arguments

ped

data.frame of pedigree in "simple" format (Three columns for ANIMAL, MOTHER and FATHER) or in "plink" format (Five to Six columns for FAMILY, ANIMAL, FATHER, MOTHER, SEX and Phenotype, where the phenotype column is optional). Is formatted within this function using pedigree.format()

pedigree.type

Character. "simple" or "plink"

cM

Numeric vector of sex-averaged map distances in centiMorgans. Not required if sex specific map distances are defined. First position should be given as 0cM

cM.male

Numeric vector of Male map distances in centiMorgans

cM.female

Numeric vector of Female map distances in centiMorgans

founder.mafs

Numeric vector of Minor allele frequencies for each marker

chromosome.ids

Vector of chromosome or linkage group IDs for each marker

snp.names

Optional character vector of SNP names

map.distances

Optional vector of map distances in base pairs for GenABEL object. Not used in the simulation.

error.rate

numeric. Default is 1e-4. Future versions will allow vector.

missing.rate

numeric. Default is 0.001. Future versions will allow vector.

xover.min.cM

numeric. Minimum cM distance between two crossovers

xover.min.cM.male

numeric. Minimum cM distance between two crossovers in males

xover.min.cM.female

numeric. Minimum cM distance between two crossovers in females


susjoh/simperSNP documentation built on May 30, 2019, 8:43 p.m.