qtl.qtlrel: Use QTLRel to map a set of traits

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

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)

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