qtcatGeno: A genotype object constructor

In QTCAT/qtcat: Quantitative Trait Cluster Association Test

Description

Constructs a S3-object containing a SNP design matrix and a hierarchy. If a SNP in the input object contains missing data, the clustering is used to impute information from highly correlated neighbor SNPs. The genotype object is needed for qtcatHit as input.

Usage

qtcatGeno(snp, snpClust, absCor, min.absCor = 0.5, mc.cores = 1)

Arguments

snp	an object of S4 class snpMatrix.
snpClust	an object of class qtcatClust.
absCor	a vector of absolute value of correlations considered in the hierarchy.
min.absCor	a minimum absolute value of correlation which is considered. A value in the range from 0 to 1.
mc.cores	a number of cores for parallelising. The maximum is 'B'. For details see mclapply.

Examples

# file containing example data for SNP data
gfile <- system.file("extdata/snpdata.csv", package = "qtcat")
snp <- read.snpData(gfile, sep = ",")
clust <- qtcatClust(snp)

# Construct geotype object
geno <- qtcatGeno(snp, clust)

QTCAT/qtcat documentation built on April 20, 2021, 11:20 p.m.