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CSSP (version 1.10.0)

ChIP-Seq Statistical Power

Description

Power computation for ChIP-Seq data based on Bayesian estimation for local poisson counting process.

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Version

Version

1.10.0

License

GPL-2

Maintainer

Chandler Zuo

Last Published

February 15th, 2017

Functions in CSSP (1.10.0)

peakpos

An artificially generated dataset containing peak invervals on 5 chromosomes.
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.
cssp.sim

Simulate bin binding intensities according to the posterior distributions of the fitted CSSP model.
pBBT

Compute the cumulative probability of the bin-level poisson parameters.
sampleFit

A "CSSPFit" class object containing the fitted CSSP model for bin.data.
bin.data

An artificially constructed BinData-class class object.
tagdat_chip

An artificially constructed dataset containing genome coordinates for aligned ChIP sample reads.
bindcount.chr

Compute the number of reads overlapping the specified positions for a single chromosome.
readBinFile

Read the bin-level text files containing ChIP and input sample counts as well as M and GC scores.
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.
createBinData

Create a BinData object by merging lists of ChIP and input bin data with external M and GC text files.
callpeak

Call enriched bins based on the CSSP model.
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.
bindpos

An artificially constructed dataset containing enrichment positions on 5 chromosomes.
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.
CSSPFit-class

An S-4 class containing the model fit information for CSSP model.
qBBT

Compute the quantile estimate for the bin-level poisson parameters.
fit.freq

Compute the estimated frequency for ChIP counts based on the CSSP model.
BinData-class

An S-4 class containing the model fit information for a CSSP model.
tagdat_input

An artificially constructed dataset containing genome coordinates for aligned input sample reads.