BinData-class           An S-4 class containing the model fit
                        information for a CSSP model.
CSSPFit-class           An S-4 class containing the model fit
                        information for CSSP model.
bin.data                An artificially constructed BinData-class class
                        object.
bindata.chr1            An artificially constructed data.frame object
                        that can be used by cssp.fit function.
bindcount               Compute the number of reads overlapping the
                        specified positions for the whole genome.
bindcount.chr           Compute the number of reads overlapping the
                        specified positions for a single chromosome.
bindpos                 An artificially constructed dataset containing
                        enrichment positions on 5 chromosomes.
callpeak                Call enriched bins based on the CSSP model.
createBinData           Create a BinData object by merging lists of
                        ChIP and input bin data with external M and GC
                        text files.
cssp.fit                Fit the CSSP Model.
cssp.power              Compute the weighted average of bin-wise power
                        conditioning on the fold change and minimal
                        ChIP count requirements.
cssp.sim                Simulate bin binding intensities according to
                        the posterior distributions of the fitted CSSP
                        model.
fit.freq                Compute the estimated frequency for ChIP counts
                        based on the CSSP model.
pBBT                    Compute the cumulative probability of the
                        bin-level poisson parameters.
peakcount               Compute the number of aligned reads overlapping
                        the specified peak intervals for the whole
                        genome.
peakcount.chr           Compute the number of aligned reads overlapping
                        peaks for one chromosome.
peakpos                 An artificially generated dataset containing
                        peak invervals on 5 chromosomes.
qBBT                    Compute the quantile estimate for the bin-level
                        poisson parameters.
readBinFile             Read the bin-level text files containing ChIP
                        and input sample counts as well as M and GC
                        scores.
sampleFit               A "CSSPFit" class object containing the fitted
                        CSSP model for bin.data.
tag2bin                 Convert the genome coordinates of aligned reads
                        to bin-level counts for all chromosomes.
tag2bin.chr             Convert the genome coordinates of aligned reads
                        to bin-level counting data for a single
                        chromosome.
tagdat_chip             An artificially constructed dataset containing
                        genome coordinates for aligned ChIP sample
                        reads.
tagdat_input            An artificially constructed dataset containing
                        genome coordinates for aligned input sample
                        reads.
