Polyfit: Add-on to DESeq to improve p-values and q-values

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Polyfit is an add-on to the packages DESeq which ensures the p-value distribution is uniform over the interval [0, 1] for data satisfying the null hypothesis of no differential expression, and uses an adpated Storey-Tibshiran method to calculate q-values.

Author
Conrad Burden
Date of publication
None
Maintainer
Conrad Burden <conrad.burden@anu.edu.au>
License
GPL (>= 3)
Version
1.8.0

View on Bioconductor

Man pages

levelPValues
Level P-values
pfNbinomTest
The Polyfit extension to the DESeq functions nbinomTest() and...
Polyfit-package
Polyfit add-on to DESeq
twoSidedPValueFromDiscrete
Two sided P-value from discrete distribution

Files in this package

Polyfit/DESCRIPTION
Polyfit/NAMESPACE
Polyfit/R
Polyfit/R/PolyfitFunctions.R
Polyfit/README.md
Polyfit/build
Polyfit/build/vignette.rds
Polyfit/inst
Polyfit/inst/doc
Polyfit/inst/doc/polyfit.R
Polyfit/inst/doc/polyfit.Rnw
Polyfit/inst/doc/polyfit.pdf
Polyfit/man
Polyfit/man/Polyfit-package.Rd
Polyfit/man/levelPValues.Rd
Polyfit/man/pfNbinomTest.Rd
Polyfit/man/twoSidedPValueFromDiscrete.Rd
Polyfit/vignettes
Polyfit/vignettes/polyfit.Rnw
Polyfit/vignettes/polyfitFig1.pdf
Polyfit/vignettes/polyfitFig4.pdf