qtl.qtlrel {DOQTL} | R Documentation

## Use QTLRel to map a set of traits

### Description

This function accepts phenotypes, genotype probabilities and a sample kinship matrix and maps the requested traits using an eight state linear model. FALSEixed covariates may be passed in as well. The output is written to two files: *.LOD.txt (containing the LOD scores for each SNP) and *.coef.txt. (containing the model coefficient at each SNP).

### Usage

      qtl.qtlrel(pheno, probs, K, addcovar, intcovar, snps)

### Arguments

`pheno` | Data frame, containing the sample IDs, phenotype data and covariates.
`probs` | 3D numeric array, containing the genotype probabilities for all samples at each SNP. Dimensions must be samples by states by SNPs and all dimensions must be named.
`K` | Numeric matrix, containing the kinship between individuals as computed by QTLRel.
`addcovar` | Numeric matrix containing additive covariates.
`intcovar` | Numeric matrix containing covariates that interact with the QTL.
`snps` | Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively.

### Value

A list containing two elements:

`lod` | Data.frame containing the SNP locations and LOD and p-values.
`coef` | Data.frame containing the model coefficients.

### Author(s)

Daniel Gatti

### See Also

`plot.doqtl`, `scanone`, `scanone.perm`

### Examples

      ## Not run:
        qtl.qtlrel(pheno, prob, K, covar = NULL, pheno.name = "")

    ## End(Not run)

[Package DOQTL version 1.16.2 Index]