$-method | MatrixList object |
coefficients-method | dmDSfit object |
colnames-method | MatrixList object |
colnames<--method | MatrixList object |
common_precision | dmDSprecision object |
common_precision-method | dmDSprecision object |
common_precision-method | dmSQTLprecision object |
common_precision<- | dmDSprecision object |
common_precision<--method | dmDSprecision object |
counts-method | dmDSdata object |
counts-method | dmSQTLdata object |
design-method | dmDSfit object |
design-method | dmDSprecision object |
design-method | dmDStest object |
dim-method | MatrixList object |
dmDSdata | Create dmDSdata object |
dmDSdata-class | dmDSdata object |
dmDSfit-class | dmDSfit object |
dmDSprecision-class | dmDSprecision object |
dmDStest-class | dmDStest object |
dmFilter | Filtering |
dmFilter-method | Filtering |
dmFit | Fit the Dirichlet-multinomial and/or the beta-binomial full model regression |
dmFit-method | Fit the Dirichlet-multinomial and/or the beta-binomial full model regression |
dmPrecision | Estimate the precision parameter in the Dirichlet-multinomial model |
dmPrecision-method | Estimate the precision parameter in the Dirichlet-multinomial model |
dmSQTLdata | Create dmSQTLdata object |
dmSQTLdata-class | dmSQTLdata object |
dmSQTLfit-class | dmSQTLfit object |
dmSQTLprecision-class | dmSQTLprecision object |
dmSQTLtest-class | dmSQTLtest object |
dmTest | Likelihood ratio test to detect differential transcript/exon usage |
dmTest-method | Likelihood ratio test to detect differential transcript/exon usage |
dm_plotDataDSInfo | Plot the frequency of present features |
dm_plotProportions | Plot feature proportions |
elementNROWS-method | MatrixList object |
genewise_precision | dmDSprecision object |
genewise_precision-method | dmDSprecision object |
genewise_precision-method | dmSQTLprecision object |
genewise_precision<- | dmDSprecision object |
genewise_precision<--method | dmDSprecision object |
length-method | MatrixList object |
length-method | dmDSdata object |
length-method | dmSQTLdata object |
MatrixList-class | MatrixList object |
mean_expression | dmDSprecision object |
mean_expression-method | dmDSprecision object |
mean_expression-method | dmSQTLprecision 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 |
plotPrecision | Precision versus mean expression plot |
plotPrecision-method | Precision versus mean expression plot |
plotProportions | Plot feature proportions |
plotProportions-method | Plot feature proportions |
plotPValues | Plot p-value distribution |
plotPValues-method | Plot p-value distribution |
proportions | dmDSfit object |
proportions-method | dmDSfit 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 |
samples-method | dmSQTLdata object |
[-method | MatrixList object |
[-method | dmDSdata object |
[-method | dmSQTLdata object |
[[-method | MatrixList object |