CSSP: ChIP-Seq Statistical Power

Share:

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

Author
Chandler Zuo, Sunduz Keles
Date of publication
None
Maintainer
Chandler Zuo<zuo@stat.wisc.edu>
License
GPL-2
Version
1.12.0

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...

Files in this package

CSSP/DESCRIPTION
CSSP/NAMESPACE
CSSP/R
CSSP/R/base.R
CSSP/R/fit_model.R
CSSP/R/post_model.R
CSSP/R/power.R
CSSP/R/process_bin.R
CSSP/build
CSSP/build/vignette.rds
CSSP/data
CSSP/data/bin.data.RData
CSSP/data/bindata.chr1.RData
CSSP/data/bindpos.RData
CSSP/data/peakpos.RData
CSSP/data/sampleFit.RData
CSSP/data/tagdat_chip.RData
CSSP/data/tagdat_input.RData
CSSP/inst
CSSP/inst/doc
CSSP/inst/doc/cssp.R
CSSP/inst/doc/cssp.pdf
CSSP/inst/doc/cssp.rnw
CSSP/inst/tests
CSSP/inst/tests/createBinData-Ex.R
CSSP/inst/tests/test-cssp.fit.R
CSSP/inst/tests/test-readdata.R
CSSP/man
CSSP/man/BinData-class.Rd
CSSP/man/CSSPFit-class.Rd
CSSP/man/bin.data.Rd
CSSP/man/bindata.chr1.Rd
CSSP/man/bindcount.Rd
CSSP/man/bindcount.chr.Rd
CSSP/man/bindpos.Rd
CSSP/man/callpeak-methods.Rd
CSSP/man/createBinData.Rd
CSSP/man/cssp.fit-methods.Rd
CSSP/man/cssp.power-methods.Rd
CSSP/man/cssp.sim-methods.Rd
CSSP/man/fit.freq-methods.Rd
CSSP/man/pBBT-methods.Rd
CSSP/man/peakcount.Rd
CSSP/man/peakcount.chr.Rd
CSSP/man/peakpos.Rd
CSSP/man/qBBT-methods.Rd
CSSP/man/readBinFile.Rd
CSSP/man/sampleFit.Rd
CSSP/man/tag2bin.Rd
CSSP/man/tag2bin.chr.Rd
CSSP/man/tagdat_chip.Rd
CSSP/man/tagdat_input.Rd
CSSP/src
CSSP/src/bincount.c
CSSP/src/binpower.c
CSSP/src/gridLogMean.c
CSSP/src/gridMGC.c
CSSP/src/gridMean.c
CSSP/src/gridMode.c
CSSP/src/gridNonpa.c
CSSP/src/gridSample.c
CSSP/src/tag2bin.c
CSSP/tests
CSSP/tests/run_tests.R
CSSP/tests/testthat
CSSP/tests/testthat/test-cssp.fit.R
CSSP/tests/testthat/test-readdata.R
CSSP/vignettes
CSSP/vignettes/cssp.rnw
CSSP/vignettes/csspRef.bib