## ----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()