## ------------------------------------------------------------------------
library(fCI)
suppressWarnings(library(fCI))
suppressWarnings(library(psych))

## ----eval=FALSE----------------------------------------------------------
## source("http://bioconductor.org/biocLite.R")
## biocLite("fCI")
## library(fCI)

## ----, results='asis'----------------------------------------------------
fci.data=data.frame(matrix(sample(3:100, 1043*6, replace=TRUE), 1043,6))

## ------------------------------------------------------------------------
 suppressWarnings(library(gtools))
 targets=fCI.call.by.index(c(1,2,3), c(4,5,6), fci.data)
 head(targets)

## ------------------------------------------------------------------------
  fci=new("NPCI")

## ----eval=FALSE----------------------------------------------------------
## fci@sample.data.normalized=fci.data**

## ----eval=FALSE----------------------------------------------------------
## **fci@sample.data.file="c://home//fci_data.txt"**

## ------------------------------------------------------------------------
if(dim(fci.data)[1]>0){
  fci@sample.data.normalized=fci.data
}

## ------------------------------------------------------------------------
if(dim(fci.data)[1]>0){
    fci=initialize(fci)
    fci@wt.index=c(1,2)
    fci@df.index=c(1,4)
}

## ------------------------------------------------------------------------
if(dim(fci.data)[1]>0){
fci =populate(fci )
fci =compute(fci )
fci =summarize(fci )
}

## ------------------------------------------------------------------------
if(dim(fci.data)[1]>0){
fci@fold.cutoff.list=list(seq(from=1.2, to=5, by=0.2))
fci@wt.index=c(2,3)
fci@df.index=c(2,5)
}

## ------------------------------------------------------------------------
fci=new("NPCI")

filename=""
if(file.exists("../inst/extdata/Supp_Dataset_part_2.txt")){
  filename="../inst/extdata/Supp_Dataset_part_2.txt"
}else if(file.exists("../../inst/extdata/Supp_Dataset_part_2.txt")){
  filename="../../inst/extdata/Supp_Dataset_part_2.txt"
}

if(nchar(filename)>3){
  fci=find.fci.targets(fci, c(1,2,3), c(4,5,6), 
                       filename,
                       use.normalization=FALSE)
  result=show.targets(fci)
  head(result, 20)
}

## ----eval=FALSE----------------------------------------------------------
## library(fCI)
## fci=normalization(fci)

## ------------------------------------------------------------------------
if(dim(fci@sample.data.normalized)[1]>100 & 
     dim(fci@sample.data.normalized)[2]>3){
fci@wt.index=c(1,2)
fci@df.index=c(1,4)
fci@method.option=1
fci =populate(fci )
fci =compute(fci )
fci =summarize(fci )
}

## ------------------------------------------------------------------------
if(nchar(filename)>3){
  fci=new("NPCI")
  fci=find.fci.targets(fci, c(1,2,3), c(4,5,6), 
             "../inst/extdata/Supp_Dataset_part_2.txt", 
             use.normalization=FALSE)
  result=show.targets(fci)
  head(result, 20)
}