scanone.assoc: Map the entire genome using association mapping.

Description

Use the imputed Sanger SNPs and the DO haplotype probabilities. Between each pair of markers, get the unique founder strain distribution patters (SDPs) and use the DO haplotype probabilities to compute the DO SNPs.

Usage

scanone.assoc(pheno, pheno.col, probs, K, addcovar, markers, cross = c("DO", "CC", "HS"), sdp.file, ncl)

Arguments

pheno

Data.frame containing the phenotype values in columns and samples in rows. rownames(pheno) must contain the sample IDs.

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. Num.samples by num.founders by num.markers.

List containing numeric matrices of leave-one-chromosome-out kinship values for all samples. Num.samples by num.samples.

addcovar

Numeric matrix of additive covariates.

cross

Character string indicating the type of cross. One of "DO", "CC", or "HS".

markers

Data.frame containing 4 columns with marker location information. SNP ID, chr, Mb, cM in columns 1 through 4, respectively.

sdp.file

Character string containing the full path to the condensed SDP file. This file is created using condense.sanger.snps.

ncl

Integer containing the number of cores to use for parallel execution.

Value

GRanges object containing the p-value for each SNP.

Details

This function imputes the Sanger SNPs onto DO genomes and performs association mapping. The speed relies upon a support file that is created using condense.sanger.snps. The support file is a tab-delimited, Tabix indexed file that contains the chromosome, bp position and SDP for each polymorphic Sanger SNP. It treats tri-morphic SNPs and heterozygotes as alternate alleles.

Examples

Run this code

  ## Not run:  scanone.assoc(pheno, pheno.col, probs, K, addcovar, markers, cross = c("DO", "CC", "HS"), sdp.file, ncl)