12 Dec 2010
Trying PICSn

On xhost09


0. Installed SVN PICS
Changed MakeVars to point to the GSL 'lib' and 'include' folders
Install seemed OK. 


1. Ran the converter for BED to RData
#read IP data
# 12 Dec 2010
# source("/projects/remc_bigdata/Brad/3T3L1_t1_GSM535743_H3K4me1/Brad_RawData2GD.R")
print("setwd()")
setwd("/projects/remc_bigdata/Brad/3T3L1_t1_GSM535743_H3K4me1")
#system("gunzip MM0386_H3K4me1_mouse_adult_islets.MAQ.allreads.mm9.bed.gz")
print("read.table()")
dataIP<-read.table("/projects/remc_bigdata/Brad/3T3L1_t1_GSM535743_H3K4me1/3T3L1_t1_GSM535743_H3K4me1_ChIP-seq.mm9.bed",header=F,colClass=c("character", "integer", "integer", "character"))
#system("gzip MM0386_H3K4me1_mouse_adult_islets.MAQ.allreads.mm9.bed")
names(dataIP) <- c("space", "start","end","strand")

print("convert to GenomeData format...")
library(PICS)
dataIP<-as(dataIP,"GenomeData")
#dataCTL<-as(dat.bed,"GenomeData")
print("save .RData, IP only...")
save(dataIP, file="3T3L1_t1_GSM535743_H3K4me1_ChIP-seq.mm9.RData")
#save(dataIP, dataCTL, file="3T3L1_t1_GSM535743_H3K4me1_ChIP-seq.mm9.RData")
q(save="no")


2. Installed 'multicore' package from CRAN
> install.packages("multicore")
trying URL 'http://cran.stat.sfu.ca/src/contrib/multicore_0.1-3.tar.gz'
...


3. Convert mm9 mappability data (zero tiles)
setwd("/projects/remc_bigdata/Brad/mappability")
system("gunzip mm9.fa-36.bed.gz")
dataMAP<-read.table("/projects/remc_bigdata/Brad/mappability/mm9.fa-36.bed",header=F,colClass=c("character", "integer", "integer", "real"))
#dataMAP<-read.table("/projects/remc_bigdata/Brad/mappability/mm9.fa-36.bed",header=F,colClass=c("character", "integer", "integer", "integer"))
names(dataMAP) <- c("space","start","end","mappability")
library(PICS)
#dataIP<-as(dataMAP,"GenomeData")
#dataCTL<-as(dat.bed,"GenomeData")
dataMAP<-as(dataMAP,"GenomeData")
save(dataMAP, file="mm9.mappability-36.RData")
q(save="no")


4. Use no CTL and no mappability, initially