scanone.eqtl: Mapping using the Matrix EQTL algorithm.
In DOQTL: Genotyping and QTL Mapping in DO Mice

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

MatrixEQTL uses a series of matrix operations to greatly accelerate QTL mapping. It can accomodate additive covariates and a common kinship matrix for all phenotypes.

1	scanone.eqtl(expr, probs, K, addcovar, snps, sex)

`expr`	Numeric matrix of phenotype values with samples in rows and phenotypes in columns. Rownames must contain sample IDs and colnames must contain phenotype names.
`probs`	Numeric three dimensional array containing the founder haplotype contributions. Num.samples by num.founders by num.markers.
`K`	Numeric matrix of kinship values for all samples. Num.samples by num.samples.
`addcovar`	Numeric matrix of additive covariates.
`snps`	Data.frame containing 4 columns with marker location information. SNP ID, chr, Mb, cM in columns 1 through 4, respectively.
`sex`	Character vector containing either "M" or F, indicating the sex of each sample. Used for mapping on the X chromosome.

Matrix EQTL centers and rotates the phenotype and genotype matrices using matrix operations. It only calculates the LOD score at each marker and does not provide coefficients.

Numeric matrix of LOD scores for all phenotypes and markers.

Daniel Gatti

Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Shabalin AA. Bioinformatics. 2012 May 15;28(10):1353-8.

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