# ChIP-Seq Statistical Power

## Documentation for package ‘CSSP’ version 1.1.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.