DIME: DIME (Differential Identification using Mixture Ensemble)

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A robust differential identification method that considers an ensemble of finite mixture models combined with a local false discovery rate (fdr) to analyze ChIP-seq (high-throughput genomic)data comparing two samples allowing for flexible modeling of data.

Author
Cenny Taslim <taslim.2@osu.edu>, with contributions from Dustin Potter, Abbasali Khalili and Shili Lin <shili@stat.osu.edu>.
Date of publication
2013-12-09 23:08:40
Maintainer
Cenny Taslim <taslim.2@osu.edu>
License
GPL (>= 2)
Version
1.2

View on CRAN

Man pages

DIME
DIME (Differential Identification using Mixtures Ensemble)
DIME.classify
Classification Based on The Best Model
DIME-package
DIME (Differential Identification using Mixtures Ensemble)
DIME.plot.fit
Plot Best Model Goodness of Fit
gng.classify
Classification Based on GNG Model
gng.fit
Function for Fitting GNG model parameters
gng.plot.comp
Plot GNG Individual Components
gng.plot.fit
Plot GNG Goodness of Fit
gng.plot.mix
Plot GNG Mixture Component Function
gng.plot.qq
QQ-plot of GNG model vs. observed data
huber
Huber's weight function
inudge.classify
Classification Based on iNUDGE Model
inudge.fit
Function for Fitting iNUDGE model parameters
inudge.plot.comp
Plot iNUDGE Individual Components
inudge.plot.fit
Plot iNUDGE Goodness of Fit
inudge.plot.mix
Plot iNUDGE Mixture Component Function
inudge.plot.qq
QQ-plot of GNG model vs. observed data
nudge.classify
Classification Based on NUDGE Model
nudge.fit
Function for Fitting NUDGE model parameters
nudge.plot.comp
Plot NUDGE Individual Components
nudge.plot.fit
Plot NUDGE Goodness of Fit
nudge.plot.mix
Plot NUDGE Mixture Component Function
nudge.plot.qq
QQ-plot of GNG model vs. observed data

Files in this package

DIME
DIME/src
DIME/src/ENE.c
DIME/NAMESPACE
DIME/R
DIME/R/nudge.classify.R
DIME/R/inudge.classify.R
DIME/R/nudge.fit.R
DIME/R/gng.classify.R
DIME/R/inudge.plot.qq.R
DIME/R/inudge.fit.R
DIME/R/huber.R
DIME/R/DIME.classify.R
DIME/R/nudge.plot.mix.R
DIME/R/nudge.plot.fit.R
DIME/R/inudge.plot.fit.R
DIME/R/DIME.plot.fit.R
DIME/R/inudge.plot.mix.R
DIME/R/nudge.plot.comp.R
DIME/R/DIME.R
DIME/R/nudge.plot.qq.R
DIME/R/gng.plot.mix.R
DIME/R/inudge.qq.plot.internal.R
DIME/R/gng.qq.plot.internal.R
DIME/R/gng.fit.R
DIME/R/gng.plot.comp.R
DIME/R/gng.plot.qq.R
DIME/R/inudge.plot.comp.R
DIME/R/gng.plot.fit.R
DIME/MD5
DIME/DESCRIPTION
DIME/man
DIME/man/inudge.plot.comp.Rd
DIME/man/gng.classify.Rd
DIME/man/inudge.classify.Rd
DIME/man/gng.plot.mix.Rd
DIME/man/DIME.plot.fit.Rd
DIME/man/inudge.plot.mix.Rd
DIME/man/inudge.plot.qq.Rd
DIME/man/DIME.classify.Rd
DIME/man/gng.plot.fit.Rd
DIME/man/nudge.classify.Rd
DIME/man/inudge.fit.Rd
DIME/man/gng.qq.plot.internal.rd
DIME/man/nudge.plot.comp.Rd
DIME/man/huber.Rd
DIME/man/DIME.Rd
DIME/man/nudge.plot.qq.Rd
DIME/man/DIME-package.Rd
DIME/man/gng.plot.qq.Rd
DIME/man/nudge.plot.fit.Rd
DIME/man/nudge.fit.Rd
DIME/man/gng.plot.comp.Rd
DIME/man/gng.fit.Rd
DIME/man/nudge.plot.mix.Rd
DIME/man/inudge.plot.fit.Rd
DIME/man/inudge.qq.plot.internal.rd