## ----R_hide002, echo=TRUE, eval=TRUE, results='tex'--------------------------- library(OpenStats) ################### # Data preparation ################### fileCon <- system.file("extdata", "test_continuous.csv", package = "OpenStats" ) read.csv(fileCon, as.is = TRUE)[60:75, c( "external_sample_id", "biological_sample_group", "sex", "age_in_days" )] ## ----R_hide003, results='tex', echo=TRUE, eval=TRUE--------------------------- ####################################### # Default behaviour with messages ####################################### library(OpenStats) fileCon <- system.file("extdata", "test_continuous.csv", package = "OpenStats" ) test_Cont <- OpenStatsList( dataset = read.csv(fileCon), testGenotype = "experimental", refGenotype = "control", dataset.colname.genotype = "biological_sample_group", dataset.colname.batch = "date_of_experiment", dataset.colname.lifestage = NULL, dataset.colname.weight = "weight", dataset.colname.sex = "sex" ) ####################################### # OpenStatsLis behaviour without messages ####################################### fileCon <- system.file("extdata", "test_continuous.csv", package = "OpenStats" ) test_Cont <- OpenStatsList( dataset = read.csv(fileCon), testGenotype = "experimental", refGenotype = "control", dataset.colname.genotype = "biological_sample_group", dataset.colname.batch = "date_of_experiment", dataset.colname.lifestage = NULL, dataset.colname.weight = "weight", dataset.colname.sex = "sex", debug = FALSE ) # No output printed ## ----R_hide005, echo=TRUE, eval=TRUE, results='tex'--------------------------- library(OpenStats) df <- read.csv(system.file("extdata", "test_continuous.csv", package = "OpenStats" )) OpenStatsList <- OpenStatsList( dataset = df, testGenotype = "experimental", refGenotype = "control", dataset.colname.batch = "date_of_experiment", dataset.colname.genotype = "biological_sample_group", dataset.colname.sex = "sex", dataset.colname.weight = "weight", debug = FALSE ) p <- plot(OpenStatsList, vars = c("Sex", "Genotype", "data_point"), ask = TRUE) # Plot categorical variables p$Categorical # plot continuous variable p$Continuous summary(OpenStatsList, style = "grid", varnumbers = FALSE, # See more options ?summarytools::dfSummary graph.col = FALSE, # Do not show the graph column valid.col = FALSE, vars = c("Sex", "Genotype", "data_point") ) ## ----R_hide01021, results='tex', echo=TRUE, eval=TRUE------------------------- library(OpenStats) ################# # Data preparation ################# ################# # Continuous data - Creating OpenStatsList object ################# fileCon <- system.file("extdata", "test_continuous.csv", package = "OpenStats" ) test_Cont <- OpenStatsList( dataset = read.csv(fileCon), testGenotype = "experimental", refGenotype = "control", dataset.colname.genotype = "biological_sample_group", dataset.colname.batch = "date_of_experiment", dataset.colname.lifestage = NULL, dataset.colname.weight = "weight", dataset.colname.sex = "sex", debug = FALSE ) ################# # Reference range framework ################# RR_result <- OpenStatsAnalysis( OpenStatsList = test_Cont, method = "RR", RR_formula = data_point ~ Genotype + Sex, debug = FALSE ) lapply(RR_result, names) # lapply(RR_result$output,names) ## ----R_hide010, results='tex', echo=TRUE, eval=TRUE--------------------------- library(OpenStats) ################# # Data preparation ################# ################# # Continuous data - Creating OpenStatsList object ################# fileCon <- system.file("extdata", "test_continuous.csv", package = "OpenStats" ) test_Cont <- OpenStatsList( dataset = read.csv(fileCon), testGenotype = "experimental", refGenotype = "control", dataset.colname.genotype = "biological_sample_group", dataset.colname.batch = "date_of_experiment", dataset.colname.lifestage = NULL, dataset.colname.weight = "weight", dataset.colname.sex = "sex", debug = FALSE ) ################# # LinearMixed model (MM) framework ################# MM_result <- OpenStatsAnalysis( OpenStatsList = test_Cont, method = "MM", MM_fixed = data_point ~ Genotype + Weight ) ## ----R_hide010m2, results='tex', echo=TRUE, eval=TRUE------------------------- library(OpenStats) ################# # Data preparation ################# ################# # Continuous data - Creating OpenStatsList object ################# fileCon <- system.file("extdata", "test_continuous.csv", package = "OpenStats" ) test_Cont <- OpenStatsList( dataset = read.csv(fileCon), testGenotype = "experimental", refGenotype = "control", dataset.colname.genotype = "biological_sample_group", dataset.colname.batch = "date_of_experiment", dataset.colname.lifestage = NULL, dataset.colname.weight = "weight", dataset.colname.sex = "sex", debug = FALSE ) ################# # LinearMixed model (MM) framework ################# MM_result <- OpenStatsAnalysis( OpenStatsList = test_Cont, method = "MM", MM_fixed = data_point ~ Genotype + Weight, debug = FALSE ) # SplitEffect estimation with respect to the Sex levels Spliteffect <- OpenStatsComplementarySplit( object = MM_result, variables = "Sex" ) class(Spliteffect) ## ----R_hide01020, results='tex', echo=TRUE, eval=TRUE------------------------- library(OpenStats) ################# # Data preparation ################# ################# # Continuous data - Creating OpenStatsList object ################# fileCon <- system.file("extdata", "test_continuous.csv", package = "OpenStats" ) test_Cont <- OpenStatsList( dataset = read.csv(fileCon), testGenotype = "experimental", refGenotype = "control", dataset.colname.genotype = "biological_sample_group", dataset.colname.batch = "date_of_experiment", dataset.colname.lifestage = NULL, dataset.colname.weight = "weight", dataset.colname.sex = "sex", debug = FALSE ) ################# # Reference range framework ################# RR_result <- OpenStatsAnalysis( OpenStatsList = test_Cont, method = "RR", RR_formula = data_point ~ Genotype + Sex ) ## ----R_hide0102, results='tex', echo=TRUE, eval=TRUE-------------------------- library(OpenStats) ################# # Categorical data - Creating OpenStatsList object ################# fileCat <- system.file("extdata", "test_categorical.csv", package = "OpenStats" ) test_Cat <- OpenStatsList( dataset = read.csv(fileCat, na.strings = "-"), testGenotype = "Aff3/Aff3", refGenotype = "+/+", dataset.colname.genotype = "Genotype", dataset.colname.batch = "Assay.Date", dataset.colname.lifestage = NULL, dataset.colname.weight = "Weight", dataset.colname.sex = "Sex", debug = FALSE ) ################# # Fisher's exact test framework ################# FE_result <- OpenStatsAnalysis( OpenStatsList = test_Cat, method = "FE", FE_formula = Thoracic.Processes ~ Genotype + Sex ) ## ----R_hide013, results='tex', echo=TRUE, eval=TRUE--------------------------- library(OpenStats) ################# # Data preparation ################# ################# # Continuous data - Creating OpenStatsList object ################# fileCon <- system.file("extdata", "test_continuous.csv", package = "OpenStats" ) test_Cont <- OpenStatsList( dataset = read.csv(fileCon), testGenotype = "experimental", refGenotype = "control", dataset.colname.genotype = "biological_sample_group", dataset.colname.batch = "date_of_experiment", dataset.colname.lifestage = NULL, dataset.colname.weight = "weight", dataset.colname.sex = "sex", debug = FALSE ) ################# # LinearMixed model (MM) framework ################# MM_result <- OpenStatsAnalysis( OpenStatsList = test_Cont, method = "MM", MM_fixed = data_point ~ Genotype + Weight, debug = FALSE ) summary(MM_result) ## ----R_hide015, results='tex', echo=TRUE, eval=TRUE--------------------------- strtrim( OpenStatsReport( object = MM_result, JSON = TRUE, RemoveNullKeys = TRUE, pretty = TRUE ), 1500 ) ## ----R_hide017, results='tex', echo=TRUE, eval=TRUE--------------------------- library(OpenStats) ################### file <- system.file("extdata", "test_continuous.csv", package = "OpenStats" ) ################### # OpenStatsList object ################### OpenStatsList <- OpenStatsList( dataset = read.csv(file), testGenotype = "experimental", refGenotype = "control", dataset.colname.batch = "date_of_experiment", dataset.colname.genotype = "biological_sample_group", dataset.colname.sex = "sex", dataset.colname.weight = "weight", debug = FALSE ) plot(OpenStatsList) summary( OpenStatsList, style = "grid", varnumbers = FALSE, # See more options ?summarytools::dfSummary graph.col = FALSE, # Do not show the graph column valid.col = FALSE ) ## ----R_hide018, results='tex', echo=TRUE, eval=TRUE--------------------------- plot(MM_result, col = 2) ## ----R_hide0175, results='tex', echo=TRUE, eval=TRUE-------------------------- sessionInfo()