fast.qtlrel {DOQTL} | R Documentation

## QTL mapping using QTLRel

### Description

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

### Usage

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

### Arguments

`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.

### Details

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

### Value

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.

### Author(s)

Daniel Gatti

### References

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.

### See Also

`scanone`, `scanone`

### Examples

      ## Not run:  fast.qtlrel(pheno, probs, K, addcovar, snps)

[Package DOQTL version 1.16.2 Index]