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