## ----global_options, include=FALSE-------------------------------------------- knitr::opts_chunk$set(fig.width=12, fig.height=8, warning=FALSE, message=FALSE) ## ----load_miRcomp------------------------------------------------------------- ## Load libraries library('miRcomp') ## ----load_example_data-------------------------------------------------------- data(lifetech) data(qpcRdefault) ## ----data_str----------------------------------------------------------------- str(lifetech) str(qpcRdefault) ## ----colnames----------------------------------------------------------------- colnames(lifetech$ct) ## ----quality_scatter---------------------------------------------------------- qualityAssessment(lifetech, plotType="scatter", label1="LifeTech AmpScore") ## ----quality_boxplot---------------------------------------------------------- qualityAssessment(lifetech, plotType="boxplot", label1="LifeTech AmpScore") ## ----quality_scatter2--------------------------------------------------------- qualityAssessment(lifetech, object2=qpcRdefault, cloglog2=TRUE, plotType="scatter", label1="LifeTech AmpScore", label2="qpcR R-squared") ## ----quality_boxplot_na------------------------------------------------------- qualityAssessment(lifetech, plotType="boxplot", na.rm=TRUE, label1="LifeTech AmpScore") ## ----complete_features-------------------------------------------------------- completeFeatures(lifetech, qcThreshold1=1.25, label1="LifeTech") ## ----complete_features2------------------------------------------------------- completeFeatures(lifetech, qcThreshold1=1.25, object2=qpcRdefault, qcThreshold2=0.99, label1="LifeTech", label2="qpcR") ## ----complete_features3------------------------------------------------------- completeFeatures(lifetech, qcThreshold1=1.25, object2=lifetech, qcThreshold2=1.4, label1="LT 1.25", label2="LT 1.4") ## ----limit_detect_boxplot----------------------------------------------------- par(mar=c(6,6,2,2)) boxes <- limitOfDetection(lifetech, qcThreshold=1.25, plotType="boxplot") str(boxes) ## ----limit_detect_scatter----------------------------------------------------- par(mfrow=c(1,3)) lods <- limitOfDetection(lifetech, qcThreshold=1.25, plotType="scatter") ## ----limit_detect_maplot------------------------------------------------------ par(mfrow=c(1,3)) lods <- limitOfDetection(lifetech, qcThreshold=1.25, plotType="MAplot") print(round(lods,digits=2)) ## ----titration_response------------------------------------------------------- titrationResponse(lifetech, qcThreshold1=1.25) ## ----titration_response2------------------------------------------------------ titrationResponse(lifetech, qcThreshold1=1.25, object2=qpcRdefault, qcThreshold2=0.99, label1="LifeTech", label2="qpcR") ## ----titration_response3------------------------------------------------------ titrationResponse(lifetech, qcThreshold1=1.25, object2=qpcRdefault, qcThreshold2=0.99, commonFeatures=FALSE, label1="LifeTech", label2="qpcR") ## ----titration_response4------------------------------------------------------ titrationResponse(lifetech, qcThreshold1=1.25, object2=lifetech, qcThreshold2=1.4, commonFeatures=FALSE, label1="AmpScore 1.25", label2="AmpScore 1.4") ## ----accuracy----------------------------------------------------------------- accuracy(lifetech, qcThreshold1=1.25) ## ----accuracy2---------------------------------------------------------------- accuracy(lifetech, qcThreshold1=1.25, object2=qpcRdefault, qcThreshold2=0.99, label1="LifeTech", label2="qpcR") ## ----accuracy3---------------------------------------------------------------- accuracy(lifetech, qcThreshold1=1.25, object2=qpcRdefault, qcThreshold2=0.99, commonFeatures=FALSE, label1="LifeTech", label2="qpcR") ## ----accuracy4---------------------------------------------------------------- accuracy(lifetech, qcThreshold1=1.25, object2=lifetech, qcThreshold2=1.4, commonFeatures=FALSE, label1="AmpScore 1.25", label2="AmpScore 1.4") ## ----precision_sd------------------------------------------------------------- boxes <- precision(lifetech, qcThreshold1=1.25, statistic="sd") str(boxes) ## ----precision_cv------------------------------------------------------------- boxes <- precision(lifetech, qcThreshold1=1.25, statistic="cv", bins=4) str(boxes) ## ----precision_sd2------------------------------------------------------------ boxes <- precision(lifetech, qcThreshold1=1.25, object2=qpcRdefault, qcThreshold2=0.99, scale="log", label1="LifeTech", label2="qpcR") str(boxes) ## ----precision_cv2------------------------------------------------------------ boxes <- precision(lifetech, qcThreshold1=1.25, object2=qpcRdefault, qcThreshold2=0.99, statistic="cv", scale="log10", label1="LifeTech", label2="qpcR") str(boxes) ## ----precision_cv3------------------------------------------------------------ boxes <- precision(lifetech, qcThreshold1=1.25, object2=qpcRdefault, qcThreshold2=0.99, commonFeatures=FALSE, statistic="cv", scale="log10", label1="LifeTech", label2="qpcR") str(boxes) ## ----precision_cv4------------------------------------------------------------ boxes <- precision(lifetech, qcThreshold1=1.25, object2=lifetech, qcThreshold2=1.4, commonFeatures=FALSE, statistic="cv", scale="log10", label1="AmpScore 1.25", label2="AmpScore 1.4") str(boxes) ## ----load_raw_data------------------------------------------------------------ library(miRcompData) data(miRcompData) ## ----show_raw_data------------------------------------------------------------ str(miRcompData) ## ----session_info------------------------------------------------------------- sessionInfo()