DOQTL (version 1.8.0)

qtl.LRS: QTL mapping with no kinship.

Description

These are two functions that perform QTL mapping without a kinship matrix. They use the QR decomposition to speed up the computation. Other than for a quick screen or for assessing significance thresholds, we do not recommend mapping without a kinship matrix. They are included for historical reasons

Usage

qtl.LRS(pheno, probs, snps, addcovar = NULL) permutations.qtl.LRS(pheno, probs, snps, addcovar, nperm = 1000,  return.val = c("lrs", "p"))

Arguments

pheno

Data.frame containing the phenotype data with samples in rows and phenotypes in columns. Sample IDs in rownames and phenotype names in colnames.

probs

Numeric three dimenaional array, containing the founder haplotype contributions or genotype probabilities. The sample IDs, founder letter codes and markers IDs must be in dimnames.

snps

data.frame containing 4 columns with marker location information. SNP ID, chr, Mb, cM in columns 1 through 4, respectively.

addcovar

data.frame or numeric matrix, containing any additive covariates. Sample IDs must be in rownames.

nperm

Numeric value containing the number of permutations to run.

return.val

Character string containing either "LRS" or "p", indicating the type of return statistic.

Value

List containing two elements. LRS: a data.frame containing the LOD scores. coef: numeric matrix containing model coefficients.

Details

The function performs Haley-Knott regression at the markers using the founder haplotype contributions in probs.

See Also

scanone

Examples

  ## Not run:  qtl.LRS(pheno, probs, snps, addcovar = NULL)