| bin.data | An artificially constructed BinData-class class object. |
| BinData-class | An S-4 class containing the model fit information for a CSSP model. |
| 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. |
| callpeak-method | 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.fit-method | 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.power-method | 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. |
| cssp.sim-method | Simulate bin binding intensities according to the posterior distributions of the fitted CSSP model. |
| CSSPFit-class | An S-4 class containing the model fit information for CSSP model. |
| fit.freq | Compute the estimated frequency for ChIP counts based on the CSSP model. |
| fit.freq-method | Compute the estimated frequency for ChIP counts based on the CSSP model. |
| pBBT | Compute the cumulative probability of the bin-level poisson parameters. |
| pBBT-method | 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. |
| qBBT-method | 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. |