qtl.LRS: QTL mapping with no kinship.

In dmgatti/DOQTL: Genotyping and QTL Mapping in DO Mice

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("lod", "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.

Details

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

Value

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

Author(s)

Daniel Gatti

See Also

scanone

Examples

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

dmgatti/DOQTL documentation built on April 7, 2024, 10:35 p.m.