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. |