Assigns QTL to a list of Haplotypes

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Description

AssignQTL assigns QTL to the qtl of objects of class haplotype. ListQTL returns a list of qtl which for the object of class haploList.

Usage

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

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

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