## ----include=FALSE---------------------------------------------- library(knitr) opts_chunk$set(fig.path='IWTomics-',concordance=TRUE,warning=TRUE,message=TRUE) options(width=66) ## ----installation,eval=FALSE,size="small"----------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("IWTomics",dependencies=TRUE) ## ----loading,eval=TRUE,results='hide',warning=FALSE,message=FALSE,size="small"---- library(IWTomics) ## ----ETn_dataset,eval=TRUE,echo=TRUE,results='markup',size="small"---- data(ETn_example) ETn_example ## ----ETn boxplot,eval=TRUE,echo=TRUE,fig.height=7,fig.width=10,label=ETn_boxplot,results='markup',fig.show='hide',size="small"---- plot(ETn_example,cex.main=2,cex.axis=1.2,cex.lab=1.2) ## ----ETn two samples test - mean,eval=TRUE,echo=TRUE,results='markup',size="small"---- ETn_test=IWTomicsTest(ETn_example, id_region1='ETn_fixed',id_region2='Control') adjusted_pval(ETn_test) ## ----ETn test plot,eval=TRUE,echo=TRUE,fig.height=10,fig.width=8,label=ETn_test_plot,results='markup',fig.show='hide',size="small"---- plotTest(ETn_test) ## ----ETn test plot scale 10kb,eval=TRUE,echo=TRUE,fig.height=10,fig.width=8,label=ETn_test_plot_10kb_scale,results='markup',fig.show='hide',size="small"---- adjusted_pval(ETn_test,scale_threshold=10) plotTest(ETn_test,scale_threshold=10) ## ----datasets,eval=TRUE,echo=TRUE,results='markup',size="small"---- examples_path <- system.file("extdata",package="IWTomics") datasets=read.table(file.path(examples_path,"datasets.txt"), sep="\t",header=TRUE,stringsAsFactors=FALSE) datasets ## ----feature datasets BED,eval=TRUE,echo=TRUE,results='markup',size="small"---- features_datasetsBED= read.table(file.path(examples_path,"features_datasetsBED.txt"), sep="\t",header=TRUE,stringsAsFactors=FALSE) features_datasetsBED ## ----import features from BED,eval=TRUE,echo=TRUE,results='markup',size="small"---- startBED=proc.time() regionsFeatures=IWTomicsData(datasets$regionFile, features_datasetsBED[,3:6],alignment='center', id_regions=datasets$id,name_regions=datasets$name, id_features=features_datasetsBED$id, name_features=features_datasetsBED$name, path=file.path(examples_path,'files')) endBED=proc.time() endBED-startBED ## ----feature datasets table,eval=TRUE,echo=TRUE,results='markup',size="small"---- features_datasetsTable= read.table(file.path(examples_path,"features_datasetsTable.txt"), sep="\t",header=TRUE,stringsAsFactors=FALSE) features_datasetsTable ## ----import features from table,eval=TRUE,echo=TRUE,results='markup',size="small"---- startTable=proc.time() regionsFeatures=IWTomicsData(datasets$regionFile, features_datasetsTable[,3:6],alignment='center', id_regions=datasets$id,name_regions=datasets$name, id_features=features_datasetsBED$id, name_features=features_datasetsBED$name, path=file.path(examples_path,'files')) endTable=proc.time() endTable-startTable ## ----IWTomicsData object,eval=TRUE,echo=TRUE,results='markup',size="small"---- regionsFeatures regionsFeatures_subset=regionsFeatures[c('elem1','control'),'ftr1'] regionsFeatures_subset ## ----scatterplot,eval=TRUE,echo=TRUE,fig.height=5,fig.width=5,label=scatterplot,results='markup',fig.show='hide',size="small"---- plot(regionsFeatures,type='pairs') ## ----scatterplot smooth,eval=TRUE,echo=TRUE,fig.height=5,fig.width=5,label=scatterplot_smooth,results='markup',fig.show='hide',size="small"---- plot(regionsFeatures,type='pairsSmooth',col='violet') ## ----curves,eval=TRUE,echo=TRUE,fig.height=7,fig.width=10,label=curves,results='markup',fig.show='hide',size="small"---- plot(regionsFeatures,type='curves', N_regions=lengthRegions(regionsFeatures), id_features_subset='ftr1',cex.main=2,cex.axis=1.2,cex.lab=1.2) ## ----boxplot,eval=TRUE,echo=TRUE,fig.height=7,fig.width=10,label=boxplot,results='markup',fig.show='hide',size="small"---- plot(regionsFeatures,type='boxplot', id_features_subset='ftr2',cex.main=2,cex.axis=1.2,cex.lab=1.2) ## ----one sample test - mean,eval=TRUE,echo=TRUE,results='markup',size="small"---- result1=IWTomicsTest(regionsFeatures,mu=c(0,5), id_region1='control',id_region2='', id_features_subset=c('ftr1','ftr2')) result1 adjusted_pval(result1) ## ----two samples test - mean,eval=TRUE,echo=TRUE,results='markup',size="small"---- result2_mean=IWTomicsTest(regionsFeatures, id_region1=c('elem1','elem2','elem3'), id_region2=c('control','control','control')) result2_mean adjusted_pval(result2_mean) ## ----two samples test - multiple quantiles,eval=TRUE,echo=TRUE,results='markup',size="small"---- result2_quantiles=IWTomicsTest(regionsFeatures, id_region1=c('elem1','elem2','elem3'), id_region2=c('control','control','control'), id_features_subset='ftr1', statistics='quantile',probs=c(0.25,0.75)) result2_quantiles adjusted_pval(result2_quantiles) ## ----reproducibility,eval=TRUE,echo=TRUE,results='markup',size="small"---- set.seed(16) result_rep1=IWTomicsTest(regionsFeatures, id_region1='elem1',id_region2='control', id_features_subset='ftr1') adjusted_pval(result_rep1) set.seed(16) result_rep2=IWTomicsTest(regionsFeatures, id_region1='elem1',id_region2='control', id_features_subset='ftr1') adjusted_pval(result_rep2) identical(result_rep1,result_rep2) ## ----regionsFeatures_center,eval=TRUE,echo=TRUE,fig.height=7,fig.width=10,label=boxplot_diff_length,results='markup',fig.show='hide',size="small"---- data(regionsFeatures_center) range(width(regions(regionsFeatures_center))) plot_data=plot(regionsFeatures_center,type='boxplot', id_regions_subset=c('elem1','control'), id_features_subset='ftr1',size=TRUE) plot_data$features_position_size ## ----not fully computable p-value curves,eval=TRUE,echo=TRUE,results='markup',warnings=TRUE,size="small"---- result_warning=IWTomicsTest(regionsFeatures_center, id_region1='elem1',id_region2='control', id_features_subset='ftr1') adjusted_pval(result_warning) ## ----two samples test - mean - detailed plot,eval=TRUE,echo=TRUE,fig.height=10,fig.width=8,label=detailed_plot,results='markup',fig.show='hide',size="small"---- plotTest(result2_mean,alpha=0.05,id_features_subset='ftr1') ## ----two samples test - mean - summary plot feature,eval=TRUE,echo=TRUE,fig.height=2.5,fig.width=12,label=summary_plot_2_feature,results='markup',fig.show='hide',size="small"---- plotSummary(result2_mean,alpha=0.05,groupby='feature',align_lab='Center') ## ----one samples test - mean - summary plot feature,eval=TRUE,echo=TRUE,fig.height=2.5,fig.width=12,label=summary_plot_1_feature,results='markup',fig.show='hide',size="small"---- result1_mu1=IWTomicsTest(regionsFeatures,mu=1, id_region1=c('elem1','elem2','elem3','control')) plotSummary(result1_mu1,alpha=0.05,groupby='feature',align_lab='Center') ## ----one samples test - mean - summary plot location,eval=TRUE,echo=TRUE,fig.height=2,fig.width=12,label=summary_plot_1_location,results='markup',fig.show='hide',size="small"---- plotSummary(result1_mu1,alpha=0.05,groupby='test',align_lab='Center') ## ----many tests - mean - summary plot feature,eval=TRUE,echo=TRUE,fig.height=4,fig.width=12,label=summary_plot_many_feature,results='markup',fig.show='hide',size="small"---- result_many=IWTomicsTest(regionsFeatures, id_region1=c('elem1','elem2','elem3', 'elem1','elem1','elem2', 'elem1','elem2','elem3','control'), id_region2=c(rep('control',3), 'elem2','elem3','elem3', rep('',4)), id_features_subset='ftr1') plotSummary(result_many,alpha=0.05,groupby='feature', align_lab='Center',gaps_tests=c(3,6), only_significant=TRUE) ## ----curve alignment scale,eval=TRUE,echo=TRUE,fig.height=5,fig.width=10,label=curves_scale,results='markup',fig.show='hide',size="small"---- data(regionsFeatures_scale) lengthFeatures(regionsFeatures_scale[,'ftr1']) features(regionsFeatures_scale)[['ftr1']][['elem1']][,1] plot(regionsFeatures_scale,type='curves', N_regions=lengthRegions(regionsFeatures_scale), id_features_subset='ftr1') ## ----curve alignment scale - measurements on the same grid,eval=TRUE,echo=TRUE,fig.height=7,fig.width=10,label=curves_scale_same_grid,results='markup',fig.show='hide',size="small"---- regionsFeatures_scale_smooth=smooth(regionsFeatures_scale,type='locpoly') lengthFeatures(regionsFeatures_scale_smooth[,'ftr1']) features(regionsFeatures_scale_smooth)[['ftr1']][['elem1']][,1] plot(regionsFeatures_scale_smooth,type='curves', N_regions=lengthRegions(regionsFeatures_scale_smooth), id_features_subset='ftr1') ## ----curve alignment scale - test,eval=TRUE,echo=TRUE,fig.height=2.5,fig.width=12,label=summary_plot_scale,results='markup',fig.show='hide',size="small"---- result=IWTomicsTest(regionsFeatures_scale_smooth, id_region1=c('elem1','elem2','elem3'), id_region2=c('control','control','control'), id_features_subset='ftr1') adjusted_pval(result) plotSummary(result,groupby='feature') ## ----change resolution,eval=TRUE,echo=TRUE,results='markup',size="small"---- regionsFeatures lengthFeatures(regionsFeatures) regionsFeatures_smooth=smooth(regionsFeatures,type='locpoly', resolution=c(4000,1000)) regionsFeatures_smooth lengthFeatures(regionsFeatures_smooth) ## ----selection of relevant scale,eval=TRUE,echo=TRUE,fig.height=10,fig.width=8,label=relevant_scale,results='markup',fig.show='hide',size="small"---- result_scale=IWTomicsTest(regionsFeatures_center, id_region1='elem1',id_region2='control', id_features_subset='ftr1') plotTest(result_scale,alpha=0.05,scale_threshold=8) ## ----setup,eval=TRUE,echo=TRUE,results='markup',size="small"---- sessionInfo()