AssignQTL {HaploSim} | R Documentation |
Assigns QTL.
AssignQTL(hList,nqtl = NA,frqtl = NA,sigma2qtl = NULL,shQTL = 1,scQTL = 1, nTraits = 1,overlap = 0,MAF = 0.1,rmCausSNP = TRUE)
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. |
A list of length nHaplotpes
.
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)