AssignQTL {HaploSim}R Documentation

Assigns QTL to a list of Haplotypes

Description

Assigns QTL.

Usage

AssignQTL(hList,nqtl = NA,frqtl = NA,sigma2qtl = NULL,shQTL = 1,scQTL = 1,
                      nTraits = 1,overlap = 0,MAF = 0.1,rmCausSNP = TRUE)

Arguments

hList List of haplotype objects.
nqtl If specified, the number of qtl which are placed on the genome.
frqtl If specified, the fraction of heterozygous SNP loci which become QTL.
sigma2qtl If specified, the qtl variance. If length(sigma2qtl)<nqtl, sigma2qtl is replicated until obtaining a vector of appropriate length. Can be specified as a list of length equal to nTraits.
shQTL If alpha is not specified, shQTL specifies the shape parameter of the gamma distribution from which allele substitution effects are sampled.
scQTL If alpha is not specified, scQTL specifies the scale parameter of the gamma distribution from which allele substitution effects are sampled.
nTraits The number of traits.
overlap Numeric between 0 and 1. Specifies the percantage of pleiotropic QTL.
MAF Minor Allele Frequency. Loci with maf below MAF are not considered to become QTL. Do not count for frqtl.
rmCausSNP Remove causative SNPs.

Value

A list of length nHaplotpes.

See Also

SampleHaplotype

Examples

hList <- SampleHaplotypes(nHaplotypes = 20,nLoc = 100,genDist =
1,nDec = 3) ## create objects
 hListd <- SampleHaplotypes(orig = hList,genDist = 1,nDec = 3)
hList <- AssignQTL(hList,frqtl = 0.1,MAF = 0.0)
hListd <- SampleHaplotypes(orig = hList,genDist = 1,nDec
= 3,QTL = TRUE)

[Package HaploSim version 1.8.1 Index]