## Note the program is very memory consuming.

# download example wiggle file at http://archive.gersteinlab.org/proj/tftarget/data/R_example_hg18_TFx.wig
# download Gene annotation file for human (hg18) at http://archive.gersteinlab.org/proj/tftarget/data/R_example_Human-refGene_annotation.txt
# download functions.R at http://archive.gersteinlab.org/proj/tftarget/data/functions.R




## set up your working directory as where you save the above files
#--------------------------------------------------------------
setwd("/home/cc59/TEMP/")
#--------------------------------------------------------------

## load on the R functions
source("functions.R")

## calculate weight based on wiggle file
mywigFile = "R_example_hg18_TFx.wig"
myannoFile = "R_example_Human-refGene_annotation.txt"
myoutFile = "weight_for_TFx.txt"
wig2weight(mywigFile, myannoFile, width=10000, smooth=T, myoutFile)

## calculate the Regulatory scores for all Refseq genes
mywigFile = "R_example_hg18_TFx.wig"
myannoFile = "R_example_Human-refGene_annotation.txt"
myweightFile = "weight_for_TFx.txt"
myoutFile = "Score_refseq.txt"
calscoreonwig(mywigFile, myannoFile, myweightFile, myoutFile)