scanone.eqtl:
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.
Value
Numeric matrix of LOD scores for all phenotypes and markers.
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.
References
Matrix eQTL: ultra fast eQTL analysis via large matrix operations.
Shabalin AA.
Bioinformatics. 2012 May 15;28(10):1353-8.