CSSP: ChIP-Seq Statistical Power

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

AuthorChandler Zuo, Sunduz Keles
Date of publicationNone
MaintainerChandler Zuo<zuo@stat.wisc.edu>
LicenseGPL-2
Version1.12.0

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

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