## ----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()