fast.qtlrel: QTL mapping using QTLRel

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

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) 

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