CSSP: ChIP-Seq Statistical Power

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CSSP")
AuthorChandler Zuo, Sunduz Keles
Bioconductor views Bayesian ChIPSeq QualityControl Sequencing
Date of publicationNone
MaintainerChandler Zuo<zuo@stat.wisc.edu>
LicenseGPL-2
Version1.14.0

View on Bioconductor

Man pages

bin.data: An artificially constructed BinData-class class object.

bindata.chr1: An artificially constructed data.frame object that can be...

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

bindcount: Compute the number of reads overlapping the specified...

bindcount.chr: Compute the number of reads overlapping the specified...

bindpos: An artificially constructed dataset containing enrichment...

callpeak-methods: Call enriched bins based on the CSSP model.

createBinData: Create a BinData object by merging lists of ChIP and input...

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

cssp.fit-methods: Fit the CSSP Model.

cssp.power-methods: Compute the weighted average of bin-wise power conditioning...

cssp.sim-methods: Simulate bin binding intensities according to the posterior...

fit.freq-methods: Compute the estimated frequency for ChIP counts based on the...

pBBT-methods: Compute the cumulative probability of the bin-level poisson...

peakcount: Compute the number of aligned reads overlapping the specified...

peakcount.chr: Compute the number of aligned reads overlapping peaks for one...

peakpos: An artificially generated dataset containing peak invervals...

qBBT-methods: Compute the quantile estimate for the bin-level poisson...

readBinFile: Read the bin-level text files containing ChIP and input...

sampleFit: A "CSSPFit" class object containing the fitted CSSP model for...

tag2bin: Convert the genome coordinates of aligned reads to bin-level...

tag2bin.chr: Convert the genome coordinates of aligned reads to bin-level...

tagdat_chip: An artificially constructed dataset containing genome...

tagdat_input: An artificially constructed dataset containing genome...

Functions

bin.data Man page
bindata.chr1 Man page
BinData-class Man page
bindcount Man page
bindcount.chr Man page
bindpos Man page
callpeak Man page
callpeak,CSSPFit-method Man page
createBinData Man page
cssp.fit Man page
cssp.fit,BinData-method Man page
CSSPFit-class Man page
cssp.fit,data.frame-method Man page
cssp.fit,data.frame-method,BinData-method Man page
cssp.power Man page
cssp.power,CSSPFit-method Man page
cssp.sim Man page
cssp.sim,CSSPFit-method Man page
fit.freq Man page
fit.freq,CSSPFit-method Man page
pBBT Man page
pBBT,CSSPFit-method Man page
peakcount Man page
peakcount.chr Man page
peakpos Man page
qBBT Man page
qBBT,CSSPFit-method Man page
readBinFile Man page
sampleFit Man page
tag2bin Man page
tag2bin.chr Man page
tagdat_chip Man page
tagdat_input Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.