Differentially expressed gene detection based on double Poisson model, negative binomial model or the mixture of them for RNA-seq data

[Up] [Top]

Documentation for package ‘DREAMSeq’ version 1.0

Help Pages

DREAMSeq-package Introduction to the DREAMSeq package
comCommonMeanVariance Compute the means and variances of samples
comGroupMeanVariance Compute the means and variances of samples
comPooledMeanVariance Compute the means and variances of samples
ddp Double Poisson distribution
DEGCountSet DEGCountSet object and constructors
DEGCountSet-class DEGCountSet object and constructors
dpWaldTest Wald test using double Poisson distribution
DREAMSeq The main function of DREAMSeq
estCommonDispersion Estimate common dispersion
estCommonDispersion-method Estimate common dispersion
estNormFactor Estimate normalization factors
estNormFactor-method Estimate normalization factors
estShrinkDispersion Estimate shrink dispersion
estShrinkDispersion-method Estimate shrink dispersion
exCounts Extract counts
exCounts-method Extract counts
exCounts<- Extract counts
exCounts<--method Extract counts
exDispLNMean Extract a mean of logarithmic dispersions
exDispLNMean-method Extract a mean of logarithmic dispersions
exDispLNMean<- Extract a mean of logarithmic dispersions
exDispLNMean<--method Extract a mean of logarithmic dispersions
exDispLNSd Extract a standard deviation of logarithmic dispersions
exDispLNSd-method Extract a standard deviation of logarithmic dispersions
exDispLNSd<- Extract a standard deviation of logarithmic dispersions
exDispLNSd<--method Extract a standard deviation of logarithmic dispersions
exEstDispersionMethod Extract an estimated method of dispersion
exEstDispersionMethod-method Extract an estimated method of dispersion
exEstDispersionMethod<- Extract an estimated method of dispersion
exEstDispersionMethod<--method Extract an estimated method of dispersion
exEstNormFactorMethod Extract an estimated method of normalization factors
exEstNormFactorMethod-method Extract an estimated method of normalization factors
exEstNormFactorMethod<- Extract an estimated method of normalization factors
exEstNormFactorMethod<--method Extract an estimated method of normalization factors
exFitMethod Extract a fitted method
exFitMethod-method Extract a fitted method
exFitMethod<- Extract a fitted method
exFitMethod<--method Extract a fitted method
exModel Extract a model
exModel-method Extract a model
exModel<- Extract a model
exModel<--method Extract a model
exNormFactor Extract normalization factors
exNormFactor-method Extract normalization factors
exNormFactor<- Extract normalization factors
exNormFactor<--method Extract normalization factors
exResult Extract a differential expression analysis result
exResult-method Extract a differential expression analysis result
exResult<- Extract a differential expression analysis result
exResult<--method Extract a differential expression analysis result
foxtail Foxtail dataset
headWaldTest Head of Wald test
headWaldTest-method Head of Wald test
modelPipeline Differential expression analysis pipeline for read count data
nbWaldTest Wald test using negative binomial distribution
scanMeans Scan means by a window