fast.qtlrel: QTL mapping using QTLRel
In DOQTL: Genotyping and QTL Mapping in DO Mice

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

This extracts teh core of the QTLRel algorithm for additive covariates.

1	fast.qtlrel(pheno, probs, K, addcovar, snps)

`pheno`	Data.frame containing the phenotype data. Sample IDs in rownames.
`probs`	Three dimensional numeric array containing the founder halplotype contributions. Num.samples by num.founder by num.markers. Sample IDs, founder letters and SNP IDs must be in dimnames.
`K`	Numeric matrix containing the kinship between samlpes. Sample IDs must be in rownames and colnames.
`addcovar`	Numeric matrix containing additive covariates to run in the mapping model. Sample IDs must be in rownames.
`snps`	Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively.

We extracted code from QTLRel, but removed several options to speed up the pipeline for QTL mapping with additive covariates and a kinship matrix.

List containing two elements:

`lod`	List containing two elements: A: Numeric matrix containing the SNP ID, chromosome, Mb, cM, percent variance explained, likelihood ratio statistic, log of the odd ratio, p-value and -log10(p-value) for autosomes. X: Numeric matrix containing the SNP ID, chromosome, Mb, cM, percent variance explained, likelihood ratio statistic, log of the odd ratio, p-value and -log10(p-value) for X chromosome.
`coef`	List containing two elements: A : Numeric matrix containing QTL model coefficients on autosomes. Markers in rows. X : List containing two elements for the X chromosome: FALSE : Numeric matrix containing QTL model coefficients for females. Markers in rows. M : Numeric matrix containing QTL model coefficients for males. Markers in rows.

Daniel Gatti

Cheng R, Abney M, Palmer AA, Skol AD. QTLRel: an R package for genome-wide association studies in which relatedness is a concern. BMC Genet. 2011 Jul 27;12:66.

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