A quantitative method to identify distinct binding patterns
for two biological ChIP-seq samples in different experimental conditions
USAGE
peak.method: peak calling methods, 'b': BELT, 'm': MACS1.4, 'm2': MACS2.0, 'f': FindPeaks, default is BELT
inpstr1: file name of the first ChIP sample
fmatstr1: the format of the first ChIP sample
ctl1: boolean value, if 'F', no control sample for the first ChIP sample is used if 'T', control sample is used
ctlfile1: file name of the first control sample
bin1: the bin size of the first ChIP sample, this parameter is only active when BELT is used
species1: the specie of the first ChIP sample. 'mouse' or 'human' is accepted
inpstr2: file name of the second ChIP sample
fmatstr2: the format of the second ChIP sample
ctl2: boolean value, if 'F', no control sample for the second ChIP sample is used if 'T', control sample is used
ctlfile12: file name of the second control sample
bin2: the bin size of the second ChIP sample, this parameter is only active when BELT is used
species2: the specie of the second ChIP sample. 'mouse' or 'human' is accepted
precision1: the precision parameter of BELT for the first ChIP sample
precision2: the precision parameter of BELT for the second ChIP sample
norm.method: normalization method. '1': linear normalization, '2': quantile normalization, '3': nonparametric empirical Bayes correction normalization (NEB), '4': no normalization is used
wil.pair: boolean value, if 'F', Wilcoxon rank sum test is used. if 'T', Wilcoxon signed rank test is used
p.value: P-value, the default values for P-value is 0.05
ratio: the fold change between two compared enriched regions
difference: the read difference between two compared enriched regions
binnum: the number of bins for the statistical test, the enriched regions are divided into small bins, and then the statistical test is performed on these bins
OUTPUT
SummaryInformation.txt: the summary report
BindingPattern.xls: the differential enriched regions with Shift or Only binding patterns within 100kb of a gene
GeneDesert.xls: the differential enriched regions in the gene desert (not within 100kb of a gene)
Unchanged.xls: the enriched regions with Unchanged binding patterns
WIG files (Enriched_[input file name]_[pattern.wig or desert.wig]): differential regions files for visualization by visualization software, e.g. IGB, UCSC genome browser