IWTomics-package {IWTomics} | R Documentation |
Implementation of the Interval-Wise Testing for "Omics" data, an extended version of the Interval-Wise Testing for functional data presented in Pini and Vantini (2017). This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference curve), and does not require fixing location and scale at the outset.
Marzia A Cremona, Alessia Pini, Francesca Chiaromonte, Simone Vantini
Maintainer: Marzia A Cremona <mac78@psu.edu>
A Pini and S Vantini (2017). Interval-Wise Testing for functional data. Journal of Nonparametric Statistics.
## ------------------------------------------------------------------------------------------- ## ------------------------------------------------------------------------------------------- ## EXAMPLE ON REAL DATA ## ------------------------------------------------------------------------------------------- ## ------------------------------------------------------------------------------------------- ## ETn Recombination hotspots data ## Two region datasets: ## ETns fixed 64-kb flanking regions and 64-kb control regions in mouse ## One feature measured in 1-kb windows: ## Recombination hotspots content ## ?ETn_example for details on the dataset data(ETn_example) ETn_example ## ------------------------------------------------------------------------------------------- ## PLOT DATA ## ------------------------------------------------------------------------------------------- ## Plot the pointwise boxplot and averages of the curves in ETn and control regions ## (note that the box of the pointwise boxplot is zero, but the average is not) plot(ETn_example) ## ------------------------------------------------------------------------------------------- ## PERFORM THE TEST ## ------------------------------------------------------------------------------------------- ## Two sample test to compare recombination hotspots ## in ETn regions vs control regions ETn_test=IWTomicsTest(ETn_example, id_region1='ETn_fixed',id_region2='Control') ## Adjusted p-value adjusted_pval(ETn_test) ## Plotting the test results plotTest(ETn_test) ## Adjusted p-value lowering the scale of the test adjusted_pval(ETn_test,scale_threshold=10) ## Plotting the test results, lowering the scale of the test plotTest(ETn_test,scale_threshold=10) ## Summary plot of the two sample test ## x11(12,2) plotSummary(ETn_test,groupby='feature',scale_threshold=10, align_lab='Integration site') ## ------------------------------------------------------------------------------------------- ## ------------------------------------------------------------------------------------------- ## EXAMPLE ON SIMULATED DATA ## ------------------------------------------------------------------------------------------- ## ------------------------------------------------------------------------------------------- examples_path <- system.file("extdata",package="IWTomics") ## Four region datasets: ## three different types of elements and one control datasets=read.table(file.path(examples_path,"datasets.txt"), sep="\t",header=TRUE,stringsAsFactors=FALSE) datasets ## Two different features measured in all four types regions features_datasetsTable=read.table(file.path(examples_path,"features_datasetsTable.txt"), sep="\t",header=TRUE,stringsAsFactors=FALSE) features_datasetsTable ## ------------------------------------------------------------------------------------------- ## GET DATA AND PLOT ## ------------------------------------------------------------------------------------------- ## Get genomic regions for the four region datasets, ## and the two features from Table files for each region dataset regionsFeatures=IWTomicsData(datasets$regionFile,features_datasetsTable[,3:6],'center', datasets$id,datasets$name, features_datasetsTable$id,features_datasetsTable$name, path=file.path(examples_path,'files')) ## Plot the pointwise boxplot of the curves in the different region datasets plot(regionsFeatures) ## ------------------------------------------------------------------------------------------- ## PERFORM THE TEST ## ------------------------------------------------------------------------------------------- ## Two sample test for the two features in the comparisons ## 'elem1' vs 'control', 'elem2' vs 'control' ## and 'elem3' vs 'control' regionsFeatures_test=IWTomicsTest(regionsFeatures,id_region1=c('elem1','elem2','elem3'), id_region2=c('control','control','control')) ## Adjusted p-value for each comparison and each feature adjusted_pval(regionsFeatures_test) ## Plotting the results of the two sample test plotTest(regionsFeatures_test) ## Summary plot of the two sample tests ## x11(10,5) plotSummary(regionsFeatures_test,groupby='feature',align_lab='Center')