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Run_R_code.txt
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Run_R_code.txt
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## 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)