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MAST

Model-based Analysis of Single-cell Transcriptomics

Installation Instructions

If you have previously installed the package SingleCellAssay you will want to remove it as MAST superscedes SingleCellAssay. (If both MAST and SingleCellAssay are attached, opaque S4 dispatch errors will result.) Remove it with:

 remove.packages('SingleCellAssay')

Then you may install or update MAST with: install.packages('devtools') library(devtools) install_github('RGLab/MAST') # or if you don't have a working latex setup install_github(RGLab/'MAST', build_vignettes=FALSE) vignette('MAST-intro')

New Features

gseaAfterBoot for competitive geneset analysis under variance inflation
Support tests of arbitrary contrasts using LRT/zlm.SingleCellAssay

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Version

Version

0.931

License

GPL(>= 2)

Maintainer

Greg Finak

Last Published

December 22nd, 2017

Functions in MAST (0.931)

Drop specified dimension from an array

Constructor for a FluidigmAssay

Linear Model-like Class

Likelihood Ratio Tests for SingleCellAssays

Describe a linear model hypothesis to be tested

Wrapper for lmer/glmer

Construct a SingleCellAssay from a matrix or array of expression

Wrapper for regular glm/lm

BayesGLMlike-class

Wrapper for bayesian GLM

DataLayer-class

DataLayer class

SingleCellAssay

SingleCellAssay: A constructor for an object of type SingleCellAssay.

ThresholdedNanoString-class

Holds output and diagnostics from thresholdNanoString Not intended to be called by the user.

Apply a vectorized binary operation recycling over last dimension

Bootstrap a zlmfit

Report standard deviation of et, for positive et for each gene

Report the mean et value for each gene

RNASeqAssay-class

RNASeqAssay class. Doesn't require ncells

outlierDetection

Filter an RNASeqAssay

combine,SingleCellAssay,ANY-method

Combine a SingleCellAssay and a vector, data.frame or AnnotatedDataFrame

SingleCellAssay-class

SingleCellAssay class

SingleCellAssay-package

"Tools for Single Cell Assay Analysis"

Coefficients of zero-inflated

SCASet is a set of SingleCellAssay objects or objects of its subclasses (i.e. FluidigmAssay) The constructor SCASet should be used to make objects of this class.

Get Z or T statistics and P values after running gseaAfterBoot

Accessor for cellData AnnotatedDataFrame

combine,SCASet,missing-method

Combines a SCASet into a unified SingleCellAssay

Initialize a prior to be used a prior for BayeGLMlike/BayesGLMlike2

deviance_residuals_hook

Standardized deviance residuals hook

Estimate hyperparameters for hierarchical variance model for continuous component

Exponential average

Constructs a SCASet

Do two objects conform in dimension and type?

continuous_residuals_hook

Hook to get the discrete residuals

filterLowExpressedGenes

Filter low-expressing genes

fit a zero-inflated regression

Report the proportion of expression for each gene

An S4 class to hold the output of a call to zlm

Layer management methods

burdenOfFiltering

Burden of filtering

combine,SingleCellAssay,SingleCellAssay-method

Combine two SingleCellAssay or derived classes

combined_residuals_hook

Hook to get the combined residuals

computeEtFromCt

computeEtFromCt

exprs,DataLayer-method

Get or set a matrix of measurement values in a SingleCellAssay

Selectively muffle warnings based on output

fit,LMERlike,missing-method

Gene set analysis for hurdle model

Calculate log-fold changes from hurdle model components

Accessor for cellData data.frame

discrete_residuals_hook

hHook to get the continuous residuals

Degrees of freedom of Zero inflated model

Accessor for wellKey

Which layer is active?

Set name of active layer

influence.bayesglm

influence for bayesglm objects.

Get name of active layer

length,SCASet-method

Get the length of an SCASet

plotSCAConcordance

Concordance plots of filtered single vs n-cell assays

Plot a likelihood ratio test object

split,SingleCellAssay-method

Split into SCASet

Model matrix accessor

Makes a nice BiPlot

sampleNames,SCASet-method

get the sample names in an SCASet

Hook to compute the combined residuals with treatment effects added back.

How many layers does a DataLayer have?

Report number of expressing cells per gene

lrTest,ZlmFit,character-method

Likelihood ratio test

Run a likelihood-ratio test

Bootstrap a zlmfit

plot.thresholdSCRNACountMatrix

Plot cutpoints and densities for thresholding

show,Mapping-method

split,DataLayer-method

Split a DataLayer correctly

summary,ZlmFit-method

Summarize model features from a ZlmFit object

Return a human-readable summary

Run a Wald test

Make matrix of continuous expression values, orthogonal to discrete

Accessor for featureData AnnotatedDataFrame

Filter a SingleCellAssay

lapply,SCASet-method

Apply a function to each member of a SCASet

rstandard.bayesglm

rstandard for bayesglm objects.

[[<-,DataLayer-method

Replace a section of a DataLayer

Subset a SingleCellAssay by data in cellData

[,DataLayer,ANY,ANY-method

Subset a DataLayer

[[,DataLayer-method

Extract from a DataLayer

[[,SCASet-method

Index into an SCASet object

Set active layer

melt.SingleCellAssay

Melt a rectangular array

Replace model matrix

summary.thresholdSCRNACountMatrix

Summarize the effect of thresholding

thresholdNanoString

thresholds for positive expression

Convenience function for running a zero-inflated regression

zlm.SingleCellAssay

Zero-inflated regression for SingleCellAssay

[,SCASet,ANY,ANY-method

Subset an SCASet to a smaller SCASet

[,SingleCellAssay,ANY,ANY-method

Subset a SingleCellAssay

Variance-covariance matrix for zero inflated

Vbeta Data Set, FluidigmAssay

waldTest,ZlmFit,matrix-method

Average within duplicated genes/primers

print.summaryZlmFit

Print summary of a ZlmFit

Used to compute module "scores"

Hook to return p_hat from the model

Return programmatically useful summary of a fit

summary,SingleCellAssay-method

Summarize expression parameters

thresholdSCRNACountMatrix

Threshold a count matrix using an adaptive threshold.

Convert a pair of character names to a list that can be placed into a data.table