AssignQTL: Assigns QTL to a list of Haplotypes

In HaploSim: Functions to Simulate Haplotypes

Assigns QTL to a list of Haplotypes

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

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

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)

HaploSim documentation built on Aug. 14, 2022, 1:06 a.m.