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### R code from vignette source 'PhenStat.Rnw' ################################################### ### code chunk number 1: R_hide_000 ################################################### #Sys.setenv(R_GSCMD = "C:\\Program Files\\gs\\gs9.21\\bin\\gswin64.exe") #tools::compactPDF(paths = 'C:\\Users\\hamedhm\\Google Drive\\At work\\ Publications. Shared with Terry and Jeremy\\PhenStat changes\\PhenStat_2.8.0\\PhenStat\\inst\\doc',gs_quality = "ebook") suppressPackageStartupMessages(library(PhenStat)) ################################################### ### code chunk number 2: R_hide_001 ################################################### PhenStat:::WhatIsNew() ################################################### ### code chunk number 3: R_hide002 ################################################### library(PhenStat) dataset1 <- system.file("extdata", "test1.csv", package = "PhenStat") dataset2 <- system.file("extdata", "test1.txt", package = "PhenStat") ################################################### ### code chunk number 4: R_hide003 ################################################### # Default behaviour with messages library(PhenStat) dataset1 <- system.file("extdata", "test1.csv", package = "PhenStat") test <- PhenList(dataset = read.csv(dataset1, na.strings = '-'), testGenotype = "Sparc/Sparc") # Out-messages are switched off test <- PhenList( dataset = read.csv(dataset1, na.strings = '-'), testGenotype = "Sparc/Sparc", outputMessages = FALSE ) ################################################### ### code chunk number 5: R_hide004 ################################################### library(PhenStat) dataset1 <- system.file("extdata", "test3.csv", package="PhenStat") test <- PhenList(dataset=read.csv(dataset1,na.strings = '-'), dataset.clean=TRUE, dataset.values.female=1, dataset.values.male=2, testGenotype="Mysm1/+") ################################################### ### code chunk number 6: R_hide005 ################################################### library(PhenStat) dataset1 <- system.file("extdata", "test3.csv", package="PhenStat") test <- PhenList(dataset=read.csv(dataset1,na.strings = '-'), dataset.clean=TRUE, dataset.values.female=1, dataset.values.male=2, testGenotype="Mysm1/+") PhenStat:::getDataset(test) test ################################################### ### code chunk number 7: R_hide006 ################################################### library(PhenStat) dataset2 <- system.file("extdata", "test2.csv", package="PhenStat") test2 <- PhenList(dataset=read.csv(dataset2,na.strings = '-'), testGenotype="Arid4a/Arid4a", dataset.colname.weight="Weight.Value") PhenStat:::testGenotype(test2) PhenStat:::refGenotype(test2) ################################################### ### code chunk number 8: R_hide007 (eval = FALSE) ################################################### ## file <- system.file("extdata", "test1.csv", package = "PhenStat") ## test = PhenStat:::PhenList(dataset = read.csv(file, na.strings = '-'), ## testGenotype = "Sparc/Sparc") ## PhenStatReport(test, ## depVariable = 'Bone.Area', ## open = TRUE) ################################################### ### code chunk number 9: R_hide008 ################################################### library(PhenStat) dataset1 <- system.file("extdata", "test1.csv", package="PhenStat") test <- PhenList(dataset=read.csv(dataset1,na.strings = '-'), 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 <- PhenStat:::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 <- PhenStat:::finalModel(result) summary(result) ################################################### ### code chunk number 10: R_hide009 ################################################### PhenStat:::testFinalModel(result) PhenStat:::classificationTag(result) ################################################### ### code chunk number 11: R_hide010 ################################################### file <- system.file("extdata", "test7_TFE.csv", package="PhenStat") test <- PhenList(dataset=read.csv(file,na.strings = '-'), 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 <- PhenStat:::TFDataset(test,depVariable="Cholesterol") # TF method is called result <- testDataset(test_TF, depVariable="Cholesterol", method="TF") summary(result) ################################################### ### code chunk number 12: R_hide011 ################################################### library(PhenStat) file <- system.file("extdata", "test1.csv", package="PhenStat") test <- PhenList(dataset=read.csv(file,na.strings = '-'), testGenotype="Sparc/Sparc") # RR method is called result <- testDataset(test, depVariable="Lean.Mass", method="RR") summary(result) ################################################### ### code chunk number 13: R_hide012 ################################################### library(PhenStat) dataset_cat <- system.file("extdata", "test_categorical.csv", package="PhenStat") test_cat <- PhenList(read.csv(dataset_cat,na.strings = '-'),testGenotype="Aff3/Aff3") result_cat <- testDataset(test_cat, depVariable="Thoracic.Processes", method="FE") PhenStat:::getVariable(result_cat) PhenStat:::method(result_cat) summary(result_cat) ################################################### ### code chunk number 14: R_hide013 ################################################### library(PhenStat) dataset1 <- system.file("extdata", "test1.csv", package="PhenStat") # MM framework test <- PhenList(dataset=read.csv(dataset1,na.strings = '-'), testGenotype="Sparc/Sparc",outputMessages=FALSE) result <- testDataset(test, depVariable="Lean.Mass", outputMessages=FALSE) summary(result) ################################################### ### code chunk number 15: R_hide014 ################################################### library(PhenStat) dataset_cat <- system.file("extdata", "test_categorical.csv", package="PhenStat") test2 <- PhenList(dataset=read.csv(dataset_cat,na.strings = '-'), testGenotype="Aff3/Aff3",outputMessages=FALSE) result2 <- testDataset(test2, depVariable="Thoracic.Processes", method="FE",outputMessages=FALSE) summary(result2) ################################################### ### code chunk number 16: R_hide015 ################################################### library(PhenStat) dataset_cat <- system.file("extdata", "test_categorical.csv", package="PhenStat") test_cat <- PhenList(dataset=read.csv(dataset_cat,na.strings = '-'), testGenotype="Aff3/Aff3",outputMessages=FALSE) result_cat <- testDataset(test_cat, depVariable="Thoracic.Processes", method="FE",outputMessages=FALSE) PhenStat:::vectorOutput(result_cat) ################################################### ### code chunk number 17: R_hide016 ################################################### library(PhenStat) dataset_cat <- system.file("extdata", "test_categorical.csv", package="PhenStat") test_cat <- PhenList(dataset=read.csv(dataset_cat,na.strings = '-'), testGenotype="Aff3/Aff3",outputMessages=FALSE) result_cat <- testDataset(test_cat, depVariable="Thoracic.Processes", method="FE",outputMessages=FALSE) #vectorOutputMatrices(result_cat) ################################################### ### code chunk number 18: R_hide017 ################################################### library(PhenStat) dataset_cat <- system.file("extdata", "test_categorical.csv", package="PhenStat") test_cat <- PhenList(dataset=read.csv(dataset_cat,na.strings = '-'), testGenotype="Aff3/Aff3",outputMessages=FALSE) result_cat <- testDataset(test_cat, depVariable="Thoracic.Processes", method="FE",outputMessages=FALSE) plot(result_cat) ################################################### ### code chunk number 19: R_hide018 ################################################### library(PhenStat) dataset_cat <- system.file("extdata", "test_categorical.csv", package="PhenStat") test_cat <- PhenList(dataset=read.csv(dataset_cat,na.strings = '-'), testGenotype="Aff3/Aff3",outputMessages=FALSE) result_cat <- testDataset(test_cat, depVariable="Thoracic.Processes", method="FE",outputMessages=FALSE) plot(result_cat) ################################################### ### code chunk number 20: R_hide019 ################################################### library(PhenStat) dataset1 <- system.file("extdata", "test1.csv", package="PhenStat") # MM framework test <- PhenList(dataset=read.csv(dataset1,na.strings = '-'), testGenotype="Sparc/Sparc",outputMessages=FALSE) result <- testDataset(test, depVariable="Lean.Mass", outputMessages=FALSE) PhenStat:::boxplotSexGenotype(test, depVariable="Lean.Mass", graphingName="Lean Mass") PhenStat:::scatterplotSexGenotypeBatch(test, depVariable="Lean.Mass", graphingName="Lean Mass") PhenStat:::scatterplotGenotypeWeight(test, depVariable="Bone.Mineral.Content", graphingName="BMC") # All in one #plot( # test, # depVariable = 'Lean.Mass', # type = c( # 'boxplotSexGenotype', # 'scatterplotSexGenotypeBatch', # 'scatterplotGenotypeWeight' # ) # ) ################################################### ### code chunk number 21: R_hide020 ################################################### library(PhenStat) dataset1 <- system.file("extdata", "test1.csv", package="PhenStat") # MM framework test <- PhenList(dataset=read.csv(dataset1,na.strings = '-'), testGenotype="Sparc/Sparc",outputMessages=FALSE) result <- testDataset(test, depVariable="Lean.Mass", outputMessages=FALSE) # All plots together # plot(result) PhenStat:::qqplotGenotype(result) PhenStat:::qqplotRandomEffects(result) PhenStat:::qqplotRotatedResiduals(result) PhenStat:::plotResidualPredicted(result) PhenStat:::boxplotResidualBatch(result)