The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution.
|Author||Danni Yu <firstname.lastname@example.org>, Wolfgang Huber <email@example.com> and Olga Vitek <firstname.lastname@example.org>|
|Date of publication||None|
|Maintainer||Danni Yu <email@example.com>|
|License||GPL (>= 3)|
countsTable: An Example Simulation Data
drawMA_vol: Draw MA Plot and Volcano Plot
ecdfAUC: Draw Empirical Cumulative Density Function (ECDF) plot
equalSpace: Calculate Grouped Shrinkage Estimates
exactNBtest1: Perform only one exact test under the Negative Binomial...
getAdjustDisp: Calculate Shrinkage (SH) Estimates for Dispersion
getNormFactor: Estimate size factors
getQ: Estimate the shrinkage target based on the quantiles of...
getT: Estimate the shrinkage target based on the initial estimates
getTgroup: This is an internal function used to calculate the shrinkage...
Hammer2months: An example of real experiment.
nbinomTestForMatricesSH: Exact test under Negative Binomial Test with Shrinkage...
nbTestSH: Differential Analysis based on RNA-seq experiments using...
plotDispersion: Drawing Dispersion-Mean plot.
rnbinomMV: Randomly Generate Negative Binomial Variable with parameters...
rowVars: Calculating the sample variance within each row of A matrix
sim: Generating Simulated Data
sSeq-package: Shrinkage estimation of dispersion in Negative Binomial...
Sultan: An example of real experiment.
Tuch: An example of real experiment.