# install package
install.packages("MLPAstats_0.5-5.tar.gz",repos=NULL) 

# load library
library(MLPAstats)


#
# Examples from GUI
#

gui.mlpa()



#
# Examples from command line
#


# 1. example without replicas


# load data
data(BRCA)

# prepare data
mlpa.dat<-setupMLPA(BRCAcontrols, BRCAtests, size, probes.control)

# normalization
norm.dat<-mlpaNorm(mlpa.dat, method="sum.peaks.controls") 

# visualize data
plot(norm.dat)

# analysis using REX-MLPA 
ans<-mlpa(norm.dat,"REX-MLPA")
plot(ans)
ans

# analysis using threshold approach
ans<-mlpa(norm.dat,"threshold")
ans


# 2. example with replicas

# load data
data(MLPAvalidation)

# prepare data
mlpa.dat<-setupMLPA(controls, tests, size, probes.control)

# normalization using sum of peaks from control probes
norm.dat<-mlpaNorm(mlpa.dat, method="sum.peaks.controls") 

# normalization considering replicas
norm.dat<-mlpaNorm(mlpa.dat, method="sum.peaks.controls", replicate=TRUE) 

# analysis using mixed-model
ans<-mlpa(norm.dat,"mixed-model")
plot(ans)
ans

# obtaining thresholds for each individual
getThresholds(ans)