Man pages for MAST
Model-based Analysis of Single Cell Transcriptomics
| applyFlat | Apply a vectorized binary operation recycling over last... |
| BayesGLMlike-class | Wrapper for bayesian GLM |
| bootVcov1 | Bootstrap a zlmfit |
| calcZ | Get Z or T statistics and P values after running... |
| colData-set-SingleCellAssay-DataFrame-method | Replace 'colData' |
| collectResiduals | Residual hooks and collection methods |
| computeEtFromCt | Compute the Et from the Ct |
| convertMASTClassicToSingleCellAssay | Convert a MASTClassic SingleCellAssay |
| CovFromBoots | Extract the inter-gene covariance matrices for continuous and... |
| defaultAssay | Default 'assay' returned |
| defaultPrior | Initialize a prior to be used a prior for... |
| dof | Degrees of freedom of Zero inflated model |
| Drop | Drop specified dimension from an array |
| ebayes | Estimate hyperparameters for hierarchical variance model for... |
| expavg | Exponential average |
| filterLowExpressedGenes | Filter low-expressing genes |
| fit | fit a zero-inflated regression |
| freq | Summary statistics for genes in an experiment |
| FromFlatDF | Construct a SingleCellAssay (or derived subclass) from a... |
| FromMatrix | Construct a SingleCellAssay from a matrix or array of... |
| getConcordance | Get the concordance between two experiments |
| getwellKey | Accessor for wellKey |
| 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 |
| logmean | Log mean |
| LRT | Likelihood Ratio Tests for SingleCellAssays |
| lrTest | Run a likelihood-ratio test |
| lrTest-ZlmFit-character-method | Likelihood ratio test |
| maits-dataset | MAITs data set, RNASeq |
| MAST-defunct | Defunct functions in package 'MAST' |
| mast_filter | Filter a SingleCellAssay |
| MAST-package | MAST: Model-based Analysis of Single- cell Transcriptomics |
| melt.SingleCellAssay | "Melt" a 'SingleCellAssay' matrix |
| model.matrix | Model matrix accessor |
| model.matrix-set | Replace model matrix |
| myBiplot | Makes a nice BiPlot |
| pbootVcov1 | Bootstrap a zlmfit |
| plotlrt | Plot a likelihood ratio test object |
| plotSCAConcordance | Concordance plots of filtered single vs n-cell assays |
| plot.thresholdSCRNACountMatrix | Plot cutpoints and densities for thresholding |
| predicted_sig-dataset | Predicted signatures |
| predict.ZlmFit | Return predictions from a ZlmFit object. |
| primerAverage | Average expression values for duplicated/redundant genes |
| print.summaryZlmFit | Print summary of a ZlmFit |
| read.fluidigm | Reads a Fluidigm Biomark (c. 2011) raw data file (or set of... |
| removeResponse | Remove the left hand side (response) from a formula |
| rstandard.bayesglm | rstandard for bayesglm objects. |
| SceToSingleCellAssay | Coerce a SingleCellExperiment to some class defined in MAST |
| se.coef | Return coefficient standard errors |
| show | show |
| split-SingleCellAssay-character-method | Split into 'list' |
| stat_ell | Plot confidence ellipse in 2D |
| subset-SingleCellAssay-method | Subset a 'SingleCellAssay' by cells (columns) |
| summarize | Return programmatically useful summary of a fit |
| summary-GSEATests-method | Summarize gene set enrichment tests |
| summary.thresholdSCRNACountMatrix | Summarize the effect of thresholding |
| summary-ZlmFit-method | Summarize model features from a 'ZlmFit' object |
| thresholdSCRNACountMatrix | Threshold a count matrix using an adaptive threshold. |
| vbeta-dataset | Vbeta Data Set |
| vbetaFA-dataset | Vbeta Data Set, FluidigmAssay |
| waldTest | Run a Wald test |
| waldTest-ZlmFit-matrix-method | Wald test |
| xform | Make matrix of continuous expression values, orthogonal to... |
| zlm | Zero-inflated regression for SingleCellAssay |
| ZlmFit-class | An S4 class to hold the output of a call to zlm |
