scanone.eqtl {DOQTL} | R Documentation

## 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)

[Package DOQTL version 1.16.2 Index]