ChIP-Seq Statistical Power

[Up] [Top]

Documentation for package ‘CSSP’ version 1.28.0

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.