qtl.LRS: QTL mapping with no kinship.
In DOQTL: Genotyping and QTL Mapping in DO Mice

Description Usage Arguments Details Value Author(s) See Also Examples

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

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

`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.