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A B C D E F G H I L M N P R S T U V W X Z misc
| MAST-package | MAST: Model-based Analysis of Single- cell Transcriptomics |
| applyFlat | Apply a vectorized binary operation recycling over last dimension |
| BayesGLMlike-class | Wrapper for bayesian GLM |
| bootVcov1 | Bootstrap a zlmfit |
| burdenOfFiltering | Filter a SingleCellAssay |
| calcZ | Get Z or T statistics and P values after running gseaAfterBoot |
| cData | Deprecated cell/feature data accessors/mutators |
| cData-method | Deprecated cell/feature data accessors/mutators |
| cData<- | Deprecated cell/feature data accessors/mutators |
| cData<--method | Deprecated cell/feature data accessors/mutators |
| coef-method | Wrapper for lmer/glmer |
| coef-method | An S4 class to hold the output of a call to zlm |
| CoefficientHypothesis | Describe a linear model hypothesis to be tested |
| colData<--method | Replace 'colData' |
| collectResiduals | Residual hooks and collection methods |
| combine-method | Deprecated cell/feature data accessors/mutators |
| combined_residuals_hook | Residual hooks and collection methods |
| computeEtFromCt | Compute the Et from the Ct |
| condmean | Summary statistics for genes in an experiment |
| condSd | Summary statistics for genes in an experiment |
| continuous_residuals_hook | Residual hooks and collection methods |
| convertMASTClassicToSingleCellAssay | Convert a MASTClassic SingleCellAssay |
| defaultPrior | Initialize a prior to be used a prior for BayeGLMlike/BayesGLMlike2 |
| deviance_residuals_hook | Residual hooks and collection methods |
| discrete_residuals_hook | Residual hooks and collection methods |
| dof | Degrees of freedom of Zero inflated model |
| dof-method | Degrees of freedom of Zero inflated model |
| Drop | Drop specified dimension from an array |
| ebayes | Estimate hyperparameters for hierarchical variance model for continuous component |
| expavg | Exponential average |
| fData | fData |
| fData-method | fData |
| featureData | Accessor for featureData 'AnnotatedDataFrame' |
| featureData-method | Accessor for featureData 'AnnotatedDataFrame' |
| filter | Filter a SingleCellAssay |
| filterLowExpressedGenes | Filter low-expressing genes |
| fit | fit a zero-inflated regression |
| fit-method | fit a zero-inflated regression |
| fitted_phat | Residual hooks and collection methods |
| FluidigmAssay | Construct a SingleCellAssay (or derived subclass) from a 'flat' (melted) data.frame/data.table |
| freq | Summary statistics for genes in an experiment |
| FromFlatDF | Construct a SingleCellAssay (or derived subclass) from a 'flat' (melted) data.frame/data.table |
| FromMatrix | Construct a SingleCellAssay from a matrix or array of expression |
| getConcordance | Get the concordance between two experiments |
| getLogFC | Calculate log-fold changes from hurdle model components |
| getrc | Get the concordance between two experiments |
| getss | Get the concordance between two experiments |
| getwellKey | Accessor for wellKey |
| getwellKey-method | Accessor for wellKey |
| getwss | Get the concordance between two experiments |
| GLMlike-class | Wrapper for regular glm/lm |
| gseaAfterBoot | Gene set analysis for hurdle model |
| GSEATests-class | An S4 class for Gene Set Enrichment output |
| hushWarning | Selectively muffle warnings based on output |
| Hypothesis | Describe a linear model hypothesis to be tested |
| impute | impute missing continuous expression for plotting |
| influence.bayesglm | Influence bayesglm object |
| invlogit | Inverse of logistic transformation |
| LMERlike-class | Wrapper for lmer/glmer |
| LMlike-class | Linear Model-like Class |
| logFC | Calculate log-fold changes from hurdle model components |
| logLik-method | Wrapper for lmer/glmer |
| logLik-method | Linear Model-like Class |
| logmean | Log mean |
| LRT | Likelihood Ratio Tests for SingleCellAssays |
| LRT-method | Likelihood Ratio Tests for SingleCellAssays |
| lrTest | Run a likelihood-ratio test |
| lrTest-method | Linear Model-like Class |
| lrTest-method | An S4 class to hold the output of a call to zlm |
| lrTest-method | Likelihood ratio test |
| maits | MAITs data set, RNASeq |
| MAST | MAST: Model-based Analysis of Single- cell Transcriptomics |
| mast_filter | Filter a SingleCellAssay |
| melt.SingleCellAssay | "Melt" a 'SingleCellAssay' matrix |
| model.matrix | Model matrix accessor |
| model.matrix-method | Model matrix accessor |
| model.matrix<- | Replace model matrix |
| myBiplot | Makes a nice BiPlot |
| numexp | Summary statistics for genes in an experiment |
| partialScore | Residual hooks and collection methods |
| pbootVcov1 | Bootstrap a zlmfit |
| plot.thresholdSCRNACountMatrix | Plot cutpoints and densities for thresholding |
| plotlrt | Plot a likelihood ratio test object |
| plotSCAConcordance | Concordance plots of filtered single vs n-cell assays |
| predict.ZlmFit | Return predictions from a ZlmFit object. |
| primerAverage | Average expression values for duplicated/redundant genes |
| print.summaryThresholdSCRNA | Summarize the effect of thresholding |
| print.summaryZlmFit | Print summary of a ZlmFit |
| read.fluidigm | Reads a Fluidigm Biomark (c. 2011) raw data file (or set of files) |
| removeResponse | Remove the left hand side (response) from a formula |
| rstandard.bayesglm | rstandard for bayesglm objects. |
| se.coef | Return coefficient standard errors |
| se.coef-method | An S4 class to hold the output of a call to zlm |
| show-method | show |
| SingleCellAssay | Construct a SingleCellAssay (or derived subclass) from a 'flat' (melted) data.frame/data.table |
| split-method | Split into 'list' |
| stat_ell | Plot confidence ellipse in 2D |
| subset-method | Subset a 'SingleCellAssay' by cells (columns) |
| summarize | Return programmatically useful summary of a fit |
| summary-method | Linear Model-like Class |
| summary-method | Summarize gene set enrichment tests |
| summary-method | Summarize model features from a 'ZlmFit' object |
| summary.thresholdSCRNACountMatrix | Summarize the effect of thresholding |
| thresholdSCRNACountMatrix | Threshold a count matrix using an adaptive threshold. |
| update-method | Wrapper for lmer/glmer |
| update-method | Linear Model-like Class |
| vbeta | Vbeta Data Set |
| vbetaFA | Vbeta Data Set, FluidigmAssay |
| vcov-method | Wrapper for regular glm/lm |
| vcov-method | Wrapper for lmer/glmer |
| vcov-method | An S4 class to hold the output of a call to zlm |
| waldTest | Run a Wald test |
| waldTest-method | Linear Model-like Class |
| waldTest-method | An S4 class to hold the output of a call to zlm |
| waldTest-method | Wald test |
| xform | Make matrix of continuous expression values, orthogonal to discrete |
| zlm | Zero-inflated regression for SingleCellAssay |
| zlm.SingleCellAssay | Zero-inflated regression for SingleCellAssay |
| ZlmFit | An S4 class to hold the output of a call to zlm |
| ZlmFit-class | An S4 class to hold the output of a call to zlm |
| "summary-ZlmFit", | Summarize model features from a 'ZlmFit' object |
| "ZlmFit-summary" | Summarize model features from a 'ZlmFit' object |