scanone: Perform a genome scan.

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

Perform a genome scan.

Description

This function is the main QTL mapping function for point mapping at each marker. The user must supply phenotypes, genotype probabilities and marker locations. Optional kinship, additive and interactive covariates may be passed in. Scanone regresses the phenotype on the genotype probabilities and produces a LOD score and founder allele effects at each marker.

Usage

  scanone(pheno, pheno.col = 1, probs, K, addcovar, intcovar, snps, model = 
  c("additive", "full"))

Arguments

pheno	data.frame containing phenotype data. Required. rownames must contain sample IDs and there must be a column labelled 'sex' to perform correct mapping on the X chromosome.
pheno.col	numeric or character vector: Either a vector of number that indicate columns to use or a set of column names in pheno.
probs	Numeric three dimensional array, containing the founder haplotype contributions or genotype probabilities. The sample IDs, founder letter codes and markers IDs must be in dimnames.
K	numeric matrix, containing the additive kinship matrix. The samples IDs must be in rownames and colnames.
addcovar	data.frame or numeric matrix, containing any additive covariates. Sample IDs must be in rownames.
intcovar	data.frame or numeric matrix, containing any covariates that interact with the QTL. Sample IDs must be in rownames.
snps	data.frame containing 4 columns with marker location information. SNP ID, chr, Mb, cM in columns 1 through 4, respectively.
model	character string, containing one of "additive" or "full", indicating the type of model to fit.

Details

We require a sex argument in addcovar for mapping on the X chromosome. This is true even if all of your samples are of the same sex. It also means that mapping on the autosomes will occur with sex as an additive covariate. See A Guide to QTL Mapping with R/qtl by Karl Broman, pages 108-118.

Value

A list containing two elements:

lod	Data.frame with nine columns containing the marker locations, LOD scores and p-values for each phenotype. Column names are SNP_ID, Chr, Mb_NCBI38, cM, perc.var, lrs, lod, p and neg.log10.p.
coef	Numeric matrix containing the founder allele effects at each locus. Colnames are the additive covariates plus the founder terms.

Author(s)

Daniel Gatti

See Also

scanone.perm

Examples

  ## Not run: scanone(pheno, pheno.col = 1, probs)

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