Package: MAST 1.33.0

Andrew McDavid

MAST: Model-based Analysis of Single Cell Transcriptomics

Methods and models for handling zero-inflated single cell assay data.

Authors:Andrew McDavid [aut, cre], Greg Finak [aut], Masanao Yajima [aut]

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MAST.pdf |MAST.html✨
MAST/json (API)
NEWS

# Install 'MAST' in R:

install.packages('MAST', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rglab/mast/issues

Datasets:

maits - MAITs data set, RNASeq
predicted_sig - Predicted signatures
vbeta - Vbeta Data Set
vbetaFA - Vbeta Data Set, FluidigmAssay

On BioConductor:MAST-1.33.0(bioc 3.21)MAST-1.32.0(bioc 3.20)

geneexpression differentialexpression genesetenrichment rnaseq transcriptomics singlecell

12.75 score 228 stars 5 packages 1.8k scripts 3.3k downloads 668 mentions 59 exports 64 dependencies

Last updated 2 months agofrom:35654e560c. Checks:OK: 1 WARNING: 4 ERROR: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 18 2024
R-4.5-win	WARNING	Dec 18 2024
R-4.5-linux	WARNING	Dec 18 2024
R-4.4-win	WARNING	Dec 18 2024
R-4.4-mac	ERROR	Dec 18 2024
R-4.3-win	WARNING	Dec 18 2024
R-4.3-mac	ERROR	Dec 18 2024

Exports:assay_idx bootVcov1 burdenOfFiltering calcZ CoefficientHypothesis colData<-collectResiduals combined_residuals_hook computeEtFromCt condmean condSd continuous_residuals_hook convertMASTClassicToSingleCellAssay defaultPrior deviance_residuals_hook discrete_residuals_hook expavg filterLowExpressedGenes fitted_phat freq FromFlatDF FromMatrix getConcordance getLogFC getrc getss getwellKey getwss gsea_control gseaAfterBoot hushWarning Hypothesis impute invlogit logFC logLik logmean LRT lrTest mast_filter melt.SingleCellAssay numexp partialScore pbootVcov1 plotSCAConcordance primerAverage read.fluidigm SceToSingleCellAssay se.coef show split stat_ell subset summary thresholdSCRNACountMatrix update vcov waldTest zlm

Dependencies:abind askpass Biobase BiocGenerics cli colorspace crayon curl data.table DelayedArray fansi farver generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable hms httr IRanges isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig plyr prettyunits progress R6 RColorBrewer Rcpp reshape2 rlang S4Arrays S4Vectors scales SingleCellExperiment SparseArray stringi stringr SummarizedExperiment sys tibble UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

MAST Intro

Andrew McDavid, Greg Finak

Rendered fromMAST-Intro.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2019-09-04
Started: 2017-08-23

Interoptability between MAST and SingleCellExperiment-derived packages.

Andrew McDavid

Rendered fromMAST-interoperability.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2023-04-20
Started: 2018-05-16

Using MAST with RNASeq: MAIT Analysis.

Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian Gersuk, Alex Shalek, Chloe K. Schlicter, Hannah W. Miller, M. Juliana McElrath, Martin Prlic, Peter Linsley, Raphael Gottardo

Rendered fromMAITAnalysis.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2020-03-21
Started: 2016-10-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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