DoubleExpSeq: Differential Exon Usage Test for RNA-Seq Data via Empirical Bayes Shrinkage of the Dispersion Parameter

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Differential exon usage test for RNA-Seq data via an empirical Bayes shrinkage method for the dispersion parameter the utilizes inclusion-exclusion data to analyze the propensity to skip an exon across groups. The input data consists of two matrices where each row represents an exon and the columns represent the biological samples. The first matrix is the count of the number of reads expressing the exon for each sample. The second matrix is the count of the number of reads that either express the exon or explicitly skip the exon across the samples, a.k.a. the total count matrix. Dividing the two matrices yields proportions representing the propensity to express the exon versus skipping the exon for each sample.

Author
Sean Ruddy
Date of publication
2015-09-04 09:25:45
Maintainer
Sean Ruddy <s.ruddy@yahoo.com>
License
GPL-3
Version
1.1

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Man pages

counts
Exon Inclusion Counts
DBGLM1
Double Binomial Generalized Linear Model with Shrinkage of...
DB.MAPlot
Plots Log-Fold Change versus Log-Concentration for...
DoubleExpSeq-package
DoubleExpSeq is a package with application to RNA-Seq...
EstimateDEBDisp
DEB-Seq: Empirical Bayes Estimates of Dispersion for a Double...
EstimateWEBDisp
WEB-Seq: Weighted Likelihood Empirical Bayes Estimates of...
exon
Toy Exon Inclusion and Total Counts Used for Examples
groups
Group Structure of the Toy Data Set
offsets
Exon Total Counts
optimPlot
Plot the WEB-Seq Maximum Likelihood Solution for the Weight...

Files in this package

DoubleExpSeq
DoubleExpSeq/NAMESPACE
DoubleExpSeq/data
DoubleExpSeq/data/exon.RData
DoubleExpSeq/R
DoubleExpSeq/R/DoubleExpSeq-internal.R
DoubleExpSeq/R/DBGLM1.R
DoubleExpSeq/R/optimPlot.R
DoubleExpSeq/R/DB.MAPlot.R
DoubleExpSeq/R/EstimateDEBDisp.R
DoubleExpSeq/R/EstimateWEBDisp.R
DoubleExpSeq/MD5
DoubleExpSeq/DESCRIPTION
DoubleExpSeq/man
DoubleExpSeq/man/DoubleExpSeq-package.Rd
DoubleExpSeq/man/EstimateDEBDisp.Rd
DoubleExpSeq/man/offsets.Rd
DoubleExpSeq/man/optimPlot.Rd
DoubleExpSeq/man/EstimateWEBDisp.Rd
DoubleExpSeq/man/counts.Rd
DoubleExpSeq/man/groups.Rd
DoubleExpSeq/man/DBGLM1.Rd
DoubleExpSeq/man/DB.MAPlot.Rd
DoubleExpSeq/man/exon.Rd