# Example of R commands to call the ROMPrev functions within R
#
# MH Roy-Gagnon
# 3/05
#
# last modified: 10/3/06


source("E:/ROMP/ROMPrev_v0.1.r")  # Defines the R functions

sink("E:/ROMP/ROMPrev_example.out") # Sends output to the specified file

# Specifies the input file.  The example data files contains 150 trios with
#  phenotype data and SNP genotype data for 3 SNPs

filename<-"E:/ROMP/ROMPrev_example.data"

# Prepares data for analyses and saves them in list object data

data<-ROMPrevPrep(filename)

# This loop runs ROMPrev and ROMPrevRS for the 3 SNPs.

for (i in 1:3) {
  res<-ROMPrev(data$y,data$xmp,data$z[,i])
  print(paste("ROMPrev, SNP",i))
  print(res)
  print(paste("ROMPrevRS, SNP",i))
  print(ROMPrevRS(data$y,data$xmp,data$z[,i],res,1000))
}

# This loop runs ROOPrev and ROOPrevRS for the 3 SNPs.

for (i in 1:3) {
  res<-ROOPrev(data$y,data$xop,data$z[,i])
  print(paste("ROOPrev, SNP",i))
  print(res)
  print(paste("ROOPrevRS, SNP",i))
  print(ROOPrevRS(data$y,data$xop,data$z[,i],res,1000))
}

sink()  # Stops sending output to file

# The results can also be saved to a file directly from the list object created
#  by the functions.  For example, the following would save the 
ROMPrev estimates,
#  standard errors, and p-values in a comma-delimited file:

out<-matrix(NA,nrow=3,ncol=7)
for (i in 1:3) {
  res<-ROMPrev(data$y,data$xmp,data$z[,i])
  out[i,1]<-res$n
  out[i,2]<-res$h2
  out[i,3]<-res$seh2
  out[i,4]<-res$ph2
  out[i,5]<-res$h2l
  out[i,6]<-res$seh2l
  out[i,7]<-res$ph2l
}
colnames(out)<-c("n","h2","seh2","ph2","h2l","seh2l","ph2l")
row.names(out)<-c("SNP1","SNP2","SNP3")
write.csv(out,file="E:/ROMP/ROMPrev_example_out.csv")

# Names of elements in list object are given in the documentation for 
each function