### R code from vignette source 'PhenStat.Rnw' ################################################### ### code chunk number 1: R.hide ################################################### library(PhenStat) dataset1 <- system.file("extdata", "test1.csv", package="PhenStat") dataset2 <- system.file("extdata", "test1.txt", package="PhenStat") ################################################### ### code chunk number 2: R.hide ################################################### # Default behaviour with messages library(PhenStat) dataset1 <- system.file("extdata", "test1.csv", package="PhenStat") test <- PhenList(dataset=read.csv(dataset1), testGenotype="Sparc/Sparc") # Out-messages are switched off test <- PhenList(dataset=read.csv(dataset1), testGenotype="Sparc/Sparc", outputMessages=FALSE) ################################################### ### code chunk number 3: R.hide ################################################### library(PhenStat) dataset1 <- system.file("extdata", "test3.csv", package="PhenStat") test <- PhenList(dataset=read.csv(dataset1), dataset.clean=TRUE, dataset.values.female=1, dataset.values.male=2, testGenotype="Mysm1/+") ################################################### ### code chunk number 4: R.hide ################################################### library(PhenStat) dataset1 <- system.file("extdata", "test1.csv", package="PhenStat") test <- PhenList(dataset=read.csv(dataset1), testGenotype="Sparc/Sparc", outputMessages=FALSE) # Default behaviour result <- testDataset(test, depVariable="Bone.Area", equation="withoutWeight") # Perform each step of the MM framework separatly result <- testDataset(test, depVariable="Bone.Area", equation="withoutWeight",callAll=FALSE) # Estimated model effects linearRegressionResults <- analysisResults(result) linearRegressionResults$model.effect.batch linearRegressionResults$model.effect.variance linearRegressionResults$model.effect.weight linearRegressionResults$model.effect.sex linearRegressionResults$model.effect.interaction # Change the effect values: interaction effect will stay in the model result <- testDataset(test, depVariable="Bone.Area", equation="withoutWeight", keepList=c(TRUE,TRUE,FALSE,TRUE,TRUE), callAll=FALSE) result <- finalModel(result) summaryOutput(result) ################################################### ### code chunk number 5: R.hide ################################################### testFinalModel(result) classificationTag(result) ################################################### ### code chunk number 6: R.hide ################################################### file <- system.file("extdata", "test7_TFE.csv", package="PhenStat") test <- PhenList(dataset=read.csv(file), testGenotype="het", refGenotype = "WT", dataset.colname.sex="sex", dataset.colname.genotype="Genotype", dataset.values.female="f", dataset.values.male= "m", dataset.colname.weight="body.weight", dataset.colname.batch="Date_of_procedure_start") # TFDataset function creates cleaned dataset - concurrent controls dataset test_TF <- TFDataset(test,depVariable="Cholesterol") # TF method is called result <- testDataset(test_TF, depVariable="Cholesterol", method="TF") summaryOutput(result) ################################################### ### code chunk number 7: R.hide ################################################### library(PhenStat) file <- system.file("extdata", "test1.csv", package="PhenStat") test <- PhenList(dataset=read.csv(file), testGenotype="Sparc/Sparc") # RR method is called result <- testDataset(test, depVariable="Lean.Mass", method="RR") summaryOutput(result) ################################################### ### code chunk number 8: R.hide ################################################### library(PhenStat) dataset_cat <- system.file("extdata", "test_categorical.csv", package="PhenStat") test_cat <- PhenList(read.csv(dataset_cat),testGenotype="Aff3/Aff3") result_cat <- testDataset(test_cat, depVariable="Thoracic.Processes", method="FE") getVariable(result_cat) method(result_cat) summaryOutput(result_cat) ################################################### ### code chunk number 9: R.hide ################################################### library(PhenStat) dataset1 <- system.file("extdata", "test1.csv", package="PhenStat") # MM framework test <- PhenList(dataset=read.csv(dataset1), testGenotype="Sparc/Sparc",outputMessages=FALSE) result <- testDataset(test, depVariable="Lean.Mass", outputMessages=FALSE) summaryOutput(result) ################################################### ### code chunk number 10: R.hide ################################################### library(PhenStat) dataset_cat <- system.file("extdata", "test_categorical.csv", package="PhenStat") test2 <- PhenList(dataset=read.csv(dataset_cat), testGenotype="Aff3/Aff3",outputMessages=FALSE) result2 <- testDataset(test2, depVariable="Thoracic.Processes", method="FE",outputMessages=FALSE) summaryOutput(result2) ################################################### ### code chunk number 11: R.hide ################################################### library(PhenStat) dataset_cat <- system.file("extdata", "test_categorical.csv", package="PhenStat") test_cat <- PhenList(dataset=read.csv(dataset_cat), testGenotype="Aff3/Aff3",outputMessages=FALSE) result_cat <- testDataset(test_cat, depVariable="Thoracic.Processes", method="FE",outputMessages=FALSE) vectorOutput(result_cat) ################################################### ### code chunk number 12: R.hide ################################################### library(PhenStat) dataset_cat <- system.file("extdata", "test_categorical.csv", package="PhenStat") test_cat <- PhenList(dataset=read.csv(dataset_cat), testGenotype="Aff3/Aff3",outputMessages=FALSE) result_cat <- testDataset(test_cat, depVariable="Thoracic.Processes", method="FE",outputMessages=FALSE) #vectorOutputMatrices(result_cat) ################################################### ### code chunk number 13: R.hide ################################################### library(PhenStat) dataset_cat <- system.file("extdata", "test_categorical.csv", package="PhenStat") test_cat <- PhenList(dataset=read.csv(dataset_cat), testGenotype="Aff3/Aff3",outputMessages=FALSE) result_cat <- testDataset(test_cat, depVariable="Thoracic.Processes", method="FE",outputMessages=FALSE) categoricalBarplot(result_cat) ################################################### ### code chunk number 14: R.hide ################################################### library(PhenStat) dataset1 <- system.file("extdata", "test1.csv", package="PhenStat") # MM framework test <- PhenList(dataset=read.csv(dataset1), testGenotype="Sparc/Sparc",outputMessages=FALSE) result <- testDataset(test, depVariable="Lean.Mass", outputMessages=FALSE) boxplotSexGenotype(test, depVariable="Lean.Mass", graphingName="Lean Mass") scatterplotSexGenotypeBatch(test, depVariable="Lean.Mass", graphingName="Lean Mass") scatterplotGenotypeWeight(test, depVariable="Bone.Mineral.Content", graphingName="BMC") ################################################### ### code chunk number 15: R.hide ################################################### library(PhenStat) dataset1 <- system.file("extdata", "test1.csv", package="PhenStat") # MM framework test <- PhenList(dataset=read.csv(dataset1), testGenotype="Sparc/Sparc",outputMessages=FALSE) result <- testDataset(test, depVariable="Lean.Mass", outputMessages=FALSE) qqplotGenotype(result) qqplotRandomEffects(result) qqplotRotatedResiduals(result) plotResidualPredicted(result) boxplotResidualBatch(result)