Differential splicing and sQTL analyses with Dirichlet-multinomial model in RNA-Seq

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Documentation for package ‘DRIMSeq’ version 1.2.0

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$-method MatrixList object
colnames-method MatrixList object
colnames<--method MatrixList object
common_dispersion dmDSdispersion object
common_dispersion-method dmDSdispersion object
common_dispersion<- dmDSdispersion object
common_dispersion<--method dmDSdispersion object
counts-method dmDSdata object
data_dmDSdata Sample data for differential splicing analysis
data_dmSQTLdata Sample data for sQTL analysis
dim-method MatrixList object
dmDispersion Estimate dispersions in Dirichlet-multinomial model
dmDispersion-method Estimate dispersions in Dirichlet-multinomial model
dmDSdata Create dmDSdata object Constructor function for a 'dmDSdata' object.
dmDSdata-class dmDSdata object
dmDSdispersion-class dmDSdispersion object
dmDSfit-class dmDSfit object
dmDStest-class dmDStest object
dmFilter Filtering
dmFilter-method Filtering
dmFit Estimate proportions in Dirichlet-multinomial model
dmFit-method Estimate proportions in Dirichlet-multinomial model
dmSQTLdata Create dmSQTLdata object
dmSQTLdata-class dmSQTLdata object
dmSQTLdataFromRanges Create dmSQTLdata object
dmSQTLdispersion-class dmSQTLdispersion object
dmSQTLfit-class dmSQTLfit object
dmSQTLtest-class dmSQTLtest object
dmTest Likelihood ratio test
dmTest-method Likelihood ratio test
dm_counts dmDSdata object
dm_counts-method dmDSdata object
dm_plotDataDSInfo Plot the frequency of present features
dm_plotProportions Plot feature proportions
dm_samples dmDSdata object
dm_samples-method dmDSdata object
elementNROWS-method MatrixList object
genewise_dispersion dmDSdispersion object
genewise_dispersion-method dmDSdispersion object
genewise_dispersion<- dmDSdispersion object
genewise_dispersion<--method dmDSdispersion object
length-method MatrixList object
length-method dmDSdata object
length-method dmSQTLdata object
MatrixList-class MatrixList object
mean_expression dmDSdispersion object
mean_expression-method dmDSdispersion object
names-method MatrixList object
names-method dmDSdata object
names-method dmSQTLdata object
names<--method MatrixList object
ncol-method MatrixList object
nrow-method MatrixList object
plotData Plot data summary
plotData-method Plot data summary
plotDispersion Dispersion versus mean expression plot
plotDispersion-method Dispersion versus mean expression plot
plotFit Plot feature proportions
plotFit-method Plot feature proportions
plotTest Plot p-values distribution
plotTest-method Plot p-values distribution
proportions dmDSfit object
proportions-method dmDSfit object
proportions-method dmDStest object
results dmDStest object
results-method dmDStest object
results-method dmSQTLtest object
rownames-method MatrixList object
rownames<--method MatrixList object
samples dmDSdata object
samples-method dmDSdata object
statistics dmDSfit object
statistics-method dmDSfit object
statistics-method dmDStest object
[-method MatrixList object
[-method dmDSdata object
[-method dmSQTLdata object
[[-method MatrixList object