hardac_r

* Writing a code: 
  - start with:
	#!/data/reddylab/software/R-3.1.2/bin/R

  - read a file:
	input_stream = file("myfile")
	bac_list = read.delim2(input_stream)
 	print(bac_list)


* Running R code in HARDAC,
sbatch -o myOutput --wrap="/data/reddylab/software/R-3.1.2/bin/R CMD BATCH myCode.r"

* Installation of packages:
  - If a package is in CRAN:
	install.packages("ggplot2", lib="/data/reddylab/YoungSook/YoungSook_software/R_pkgs/")
	library(ggplot, lib.loc="/data/reddylab/YoungSook/YoungSook_software/R_pkgs/")
  - If it is not: ex) when you have to connect to biocLite
	store it in local library(default setting) -> move all packages to /data/reddylab/YoungSook/YoungSook_software/R_pkgs/ 
	(command: mv )

* DESeq package
   - Needed packages in advance:
	BiocGenerics, Biobase, locfit