scanone.eqtl: Mapping using the Matrix EQTL algorithm.

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

Mapping using the Matrix EQTL algorithm.

Description

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.

Usage

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

Arguments

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.

Details

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.

Value

Numeric matrix of LOD scores for all phenotypes and markers.

Author(s)

Daniel Gatti

References

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

See Also

scanone

Examples

  ## Not run:  scanone.eqtl(expr, probs, K, addcovar, snps) 

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