Bay2Ctrls: bayesian model to integrate two types of ChIP-seq controls for binding site detection

This R package is based on spp-1.14. And the wrapper script (run_Bay2Ctrls.R) for the R package is adapted from the ENCODE ChIP-seq pipeline. 

INSTALLATION
R CMD INSTALL Bay2Ctrls-0.1.tar.gz

DATA INPUT
This software require one IP (i) and two set of controls:
The first control is the DNA input (di) generated for the IP experiment. This control (di) and the IP (i) are the results from conventional ChIP-seq.
The second control contains a mock IP (m) and its corresponding DNA input (dm)

DATA OUTPUT
Binding peaks are in the narrow peak file format

USAGE
R run_Bay2Ctrls.R 

# Paramters specific for Bay2Ctrls
-ip		  a *.tagAlign.gz file containing mapped reads from the IP experiment (i)
-mock		  a *.tagAlign.gz file containing mapped reads from the mock IP experiment (m)
-input4ip	  a *.tagAlign.gz file containing mapped reads from the DNA input control for the IP experiment (di)
-input4mock	  a *.tagAlign.gz file containing mapped reads from the DNA input control for the mock IP experiment (dm)
-totReads	  scaling the numbers of reads of the four experiments to the same level, e.g. -totReads=10000000
-mcstep		  simulation steps for the Bayesian model, e.g. -mcstep=1000000

# Intrinsic parameters of SPP
-npeak		  the number of total narrow peaks to be output, e.g. -npeak=30000
-x		  avoid phantom peaks, e.g. -x=-500:85
-s		  genomic distance for signal correlation, e.g. -s=0:5:1200
-out		  output log file
-rf		  remove previous results
-odir		  output directory
-p		  number of processors to be used
More options for output format please refer to the spp R package


An example of the command:
Rscript ./run_Bay2Ctrls.R -ip=test_data/a.rep0.tagAlign.gz -mock=test_data/EMb1.rep0.tagAlign.gz -input4ip=test_data/ap.rep0.tagAlign.gz -input4mock=test_data/EMb1p.rep0.tagAlign.gz -npeak=30000 -x=-500:85 -s=0:5:1200 -odir=./ -p=1 -filtchr='.*_[CD].*' -savr -savp -rf -out=test.cc -npeak=30000 -totReads=10000000 -mcstep=1000000