## ----echo=TRUE, eval=FALSE---------------------------------------------------- # devtools::install_github("izhbannikov/rqt", buildVignette=TRUE) ## ----echo=TRUE, message=FALSE------------------------------------------------- library(rqt) 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) res <- geneTest(obj, method="pca", out.type = "D") print(res) ## ----echo=TRUE, message=FALSE------------------------------------------------- library(rqt) data <- data.matrix(read.table(system.file("extdata/test.cont1.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) res <- geneTest(obj, method="pca", out.type = "C") print(res) ## ----echo=TRUE, message=FALSE------------------------------------------------- library(rqt) data <- data.matrix(read.table(system.file("extdata/test.cont1.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) res <- geneTest(obj, method="pls", out.type = "C") print(res) ## ----echo=TRUE, message=FALSE------------------------------------------------- library(rqt) 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) # Not yet supported, sorry! #res <- geneTest(obj, method="pls", out.type = "D", scale = TRUE) print(res) ## ----echo=TRUE, message=FALSE------------------------------------------------- library(rqt) 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) covars <- read.table(system.file("extdata/test.cova1.dat",package="rqt"), header=TRUE) obj <- rqt(phenotype=pheno, genotype=geno.obj, covariates = covars) res <- geneTest(obj, method="pca", out.type = "D") print(res) ## ----echo=TRUE, message=FALSE------------------------------------------------- library(rqt) data <- data.matrix(read.table(system.file("extdata/test.cont1.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) covars <- read.table(system.file("extdata/test.cova1.dat",package="rqt"), header=TRUE) obj <- rqt(phenotype=pheno, genotype=geno.obj, covariates = covars) res <- geneTest(obj, method="pca", out.type = "C") print(res) ## ----echo=TRUE, message=FALSE------------------------------------------------- library(rqt) data1 <- data.matrix(read.table(system.file("extdata/phengen2.dat", package="rqt"), skip=1)) pheno <- data1[,1] geno <- data1[, 2:dim(data1)[2]] colnames(geno) <- paste(seq(1, dim(geno)[2])) geno.obj <- SummarizedExperiment(geno) obj1 <- rqt(phenotype=pheno, genotype=geno.obj) data2 <- data.matrix(read.table(system.file("extdata/phengen3.dat", package="rqt"), skip=1)) pheno <- data2[,1] geno <- data2[, 2:dim(data2)[2]] colnames(geno) <- paste(seq(1, dim(geno)[2])) geno.obj <- SummarizedExperiment(geno) obj2 <- rqt(phenotype=pheno, genotype=geno.obj) data3 <- data.matrix(read.table(system.file("extdata/phengen.dat", package="rqt"), skip=1)) pheno <- data3[,1] geno <- data3[, 2:dim(data3)[2]] colnames(geno) <- paste(seq(1, dim(geno)[2])) geno.obj <- SummarizedExperiment(geno) obj3 <- rqt(phenotype=pheno, genotype=geno.obj) res.meta <- geneTestMeta(list(obj1, obj2, obj3)) print(res.meta) ## ----echo=TRUE---------------------------------------------------------------- sessionInfo()