rqt-methods: The rqt class constructor

In izhbannikov/rqt: rqt: utilities for gene-level meta-analysis

The rqt class constructor

Description

This function generates rqt class objects

Usage

rqt(phenotype = NULL, genotype = NULL, covariates = NULL, results = NULL)

Arguments

phenotype	Phenotype (a vector of length N, where N - number of individuals).
genotype	Genotype - an object of class SummarizedExperiment. Should contain one assay (matrix, N by M where N - number of individuals, M - number of genetic variants).
covariates	Covariates, a data frame N by K where N - number of individuals, K - number of covariates
results	A list of two: test statistics: (Q1, Q2, Q3), p-values: (p1.Q1, p2.Q2, p3.Q3)

Value

Object of class rqt

Examples

data <- data.matrix(read.table(system.file("extdata/test.bin1.dat",
package="rqt"), header=TRUE))
pheno <- data[,1]
geno <- data[, 2:dim(data)[2]]
colnames(geno) <- paste(seq(1, dim(geno)[2]))
geno.obj <- SummarizedExperiment(geno)
obj <- rqt(phenotype=pheno, genotype=geno.obj)
print(obj)

izhbannikov/rqt documentation built on Aug. 2, 2024, 1:39 p.m.