File	Date	Author	Commit
R4ChIPSEQ-1.0.0.R	2012-10-25	ahorvath	[8a49f0] - minor changes
R4ChIPSEQ-1.0.1.R	2012-10-25	ahorvath	[8a49f0] - minor changes
R4ChIPSEQ-1.0.2.R	2012-07-31	ahorvath	[d7d6f1] - minor changes
README	2012-06-29	ahorvath	[b4cc42] - add more extra MACS parameters

Read Me

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##               Random Read Reduction in R for ChIP-SEQ data                  ##
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##              Author: ahorvath (horvath.attila4444@gmail.com)                ##
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## Used statistical models:                                                    ##
##      - 3 parameter Asymtotic model: y ~ A - (B ^ x) * C                     ##
##      - Weibull model: y ~ A - (B ^ (x ^ d)) * C                             ##
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Loading required package: getopt
R4ChIPSEQ:: Treatment file is mandatory parameter. 
R4ChIPSEQ:: Usage: R4ChIPSEQ-1.0.0.R -t <treatment-file> [-c <control-file>] [-b <begin>] [-e <end>] 
       			[-o <observations>] [-n <name>] [-G <genomsize>] [-x <experiments>] 
       			[-M <macs-program>] [-m <mfold-low-limit,mfold-low-limit>] 
       			[-P <petdist>] [-s <slocal>] [-l <llocal>] [-p <pvalue>] [-w <workdir>] [-k] [-L] 
       			[-k] [-L] [-N] [-T] [-S] [-j] [-O] [-T] [-w] [-B] [-f] [-C] [-v <verbose-level>] [-d <diag>] [-f <femin>]  [-F <femax>]  [-c <femstep>]  

 Example : Rscript R4ChIPSEQ-1.0.0.R -t /path/to/bedfile.bed -o 11 -n expname -w /path/to/workdir 

 -t|--treatment <treatment-file> --> The treatment file in BED format, mandatory parameter 
 -c|--control <control-file> --> The control file in BED format, optional parameter 
 -b|--begin <begin> --> The starting point of the reduction, the value has to be in interval [0,1), optional parameter (default=0.1) 
 -e|--end <end> --> The ending point of the reduction, the value has to be in interval [0,1) and greater than value begin, optional parameter (default=1.0) 
 -o|--observations <observations> --> Defines necessary experimental points, including begin and start points 
 -n|--name <name> -->  Name of experiment, optional MACS parameter (default="NA"), see more in the MACS Manual 
 -G|--genomsize <genom-size> --> Size of genome - optional MACS parameter, see more in the MACS Manual 
 -x|--experiments <experiment-count> -->  Defines count of experiments, optional parameter (default=1) 
 -D|--dstart --> start value of d parameter in Weibull model, optional parameter (default=0.7) 
 -M|--macs <macs-program> -->  Defines count of experiments, optional parameter (default="macs") 
 -m|--mfold <m-start,mfold-end> --> Range of mfold, optional MACS parameter (default=10,30), see more in the MACS Manual 
 -p|--pvalue <p-value> -->  P-value cutoff, optional MACS parameter (default=1e-5), see more in the MAC Manual 
 -w|--workdir <workdir> --> Work directory of read reduction process 
 -k|--keepfiles --> Keeps the reduced files, optional parameter (default=false) 
 -L|--nolamba --> If true, MACS will use fixed background lambda as local lambda for every peak region, optional MACS parameter (default=false), see more in the MACS Manual 
 -N|--nomodel --> Whether or not to build the shifting model, optional MACS parameter (default=false), see more in the MACS Manual 
 -T|--tagsize --> Tag size. This will overide the auto detected tag size, optional MACS parameter (default=false), see more in the MACS Manual 
 -S|--shiftsize --> The arbitrary shift size in bp. When nomodel is true, MACS will use this value as 1/2 of fragment size, optional MACS parameter (default=100), see more in the MACS Manual 
 -j|--jump --> Jump peak calling and model building process (default=false) 
 -P|--petdist <petdist> --> Best distance between Pair-End Tags. Only available when format is "ELANDMULTIPET", optional parameter (default=200), see more in the MACS Manual 
 -s|--slocal <smalllocal> --> The small nearby region in basepairs to calculate dynamic lambda. This is used to capture the bias near the peak summit region. Invalid if there is no control data, optional MACS parameter (default=1000), see more in the MACS Manual 
 -l|--llocal <largelocal> --> The large nearby region in basepairs to calculate dynamic lambda. This is used to capture the surround bias, optional MACS parameter (default=10000), see more in the MACS Manual 
 -O|--offauto --> Whether turn off the auto pair model process. If not set, when MACS failed to build paired model, it will use the nomodel settings, the '--shiftsize' parameter to shift and extend each tags, optional MACS parameter (default=false), see more in the MACS Manual 
 --tosmall --> When set, scale the larger dataset down to the smaller dataset, by default, the smaller dataset will be scaled towards the larger dataset, optional MACS parameter (default=false),  see more in the MACS Manual 
 --wig --> Whether or not to save extended fragment pileup at every WIGEXTEND bps into a wiggle file. When --single-profile is on, only one file for the whole genome is saved. WARNING: this process is time/space consuming!!, optional MACS parameter (default=false), see more in the MACS Manual 
 -B|--bdg --> Whether or not to save extended fragment pileup at every bp into a bedGraph file. When it's on, -w, --space and --call-subpeaks will be ignored. When --single-profile is on, only one file for the whole genome is saved. WARNING: this process is time/space consuming!! Optional MACS parameter (default=false), see more in the MACS Manual 
 --singleprofile -->  When set, a single wiggle file will be saved for treatment and input. Optional MACS parameter (default=false), see more in the MACS Manual 
 --space=SPACE --> The resoluation for saving wiggle files, by default, MACS will save the raw tag count every 10 bps. Usable only with '--wig' option. Optional MACS parameter, see more in the MACS Manual 
 -C|--callsubpeaks --> If set, MACS will invoke Mali Salmon's PeakSplitter soft through system call. If PeakSplitter can't be found, an instruction will be shown for downloading and installing the PeakSplitter package. -w option needs to be on and -B should be off to let it work. Optional MACS parameter (default=false), see more in the MACS Manual 
 -v|--verbose <verbose-level> --> Set verbose level. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. Optional MACS parameter (default=2), see more in the MACS Manual 
 -d|--diag --> Whether or not to produce a diagnosis report. It's up to 9X time consuming. Please check 00README file for detail. Optional MACS parameter (default=false), see more in the MACS Manual 
 -f|--femin <femin> --> For diagnostics, min fold enrichment to consider. Optional MACS parameter (default=0), see more in the MACS Manual 
 -F|--femax <femax> --> For diagnostics, max fold enrichment to consider. Optional MACS parameter (default=maximum fold enrichment), see more in the MACS Manual 
 -r|--festep <festep> --> For diagnostics, fold enrichment step. Optional MACS parameter (default=20), see more in the MACS Manual