MAST: Model-based Analysis of Single Cell Transcriptomics
Version 1.2.1

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

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AuthorAndrew McDavid [aut, cre], Greg Finak [aut], Masanao Yajima [aut]
Bioconductor views DifferentialExpression GeneExpression GeneSetEnrichment RNASeq SingleCell Transcriptomics
Date of publicationNone
MaintainerAndrew McDavid <Andrew_McDavid@urmc.rochester.edu>
LicenseGPL(>= 2)
Version1.2.1
URL https://github.com/RGLab/MAST/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MAST")

Man pages

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...
cData: Deprecated cell/feature data accessors/mutators
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
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
fData-methods: fData
featureData-methods: Accessor for featureData 'AnnotatedDataFrame'
filter: Filter a SingleCellAssay
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-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
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.
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

Functions

BayesGLMlike-class Man page
CoefficientHypothesis Man page
Drop Man page Source code
FluidigmAssay Man page
FromFlatDF Man page Source code
FromMatrix Man page Source code
GLMlike-class Man page
GSEATests-class Man page
Glue Source code
Hypothesis Man page
LMERlike-class Man page
LMlike-class Man page
LRT Man page
LRT,SingleCellAssay,character-method Man page
MAST Man page
MAST-package Man page
SingleCellAssay Man page
ZlmFit-class Man page
applyFlat Man page Source code
apply_by Source code
approxt Source code
as3dArray Source code
bayesglm.fit Source code
bayesglm.fit.cleanup Source code
bayesglm.fit.initialize.family Source code
bayesglm.fit.initialize.other Source code
bayesglm.fit.initialize.priorScale Source code
bayesglm.fit.initialize.priors Source code
bayesglm.fit.initialize.x Source code
bayesglm.fit.loop.createAuxillaryItems Source code
bayesglm.fit.loop.initializePriors Source code
bayesglm.fit.loop.initializeState Source code
bayesglm.fit.loop.main.ideal Source code
bayesglm.fit.loop.print Source code
bayesglm.fit.loop.printWarnings Source code
bayesglm.fit.loop.setup Source code
bayesglm.fit.loop.updateState Source code
bayesglm.fit.loop.validateInputs Source code
bayesglm.fit.loop.validateState Source code
bayesglm.influence Source code
between_interval Source code
bootVcov1 Man page Source code
burdenOfFiltering Man page Source code
cData Man page
cData,SingleCellAssay-method Man page
cData<- Man page
cData<-,SingleCellAssay-method Man page
calcZ Man page Source code
callName Source code
check.vars Source code
checkArrayNames Source code
checkGroups Source code
coef,LMERlike-method Man page
coef,ZlmFit-method Man page
colData<-,SingleCellAssay,DataFrame-method Man page
collectResiduals Man page Source code
collectSummaries Source code
combine,SingleCellAssay,ANY-method Man page
combine,SingleCellAssay,SingleCellAssay-method Man page
combined_residuals_hook Man page Source code
complexifyNA Source code
computeEtFromCt Man page Source code
condSd Man page Source code
condmean Man page Source code
continuous_residuals_hook Man page Source code
convertMASTClassicToSingleCellAssay Man page Source code
defaultPrior Man page Source code
deviance_residuals_hook Man page Source code
dexpit Source code
discrete_residuals_hook Man page Source code
dispersion Source code
dof Man page
dof,GLMlike-method Man page
ebayes Man page Source code
ell Source code
escapeSymbols Source code
expavg Man page Source code
expit Source code
fData Man page
fData,SingleCellAssay-method Man page
featureData Man page
featureData,SingleCellAssay-method Man page
filter Man page Source code
filterLowExpressedGenes Man page Source code
find_peaks Source code
find_valleys Source code
fit Man page Source code
fit,GLMlike,missing-method Man page
fit,LMERlike,missing-method Man page
fitted_phat Man page Source code
fixdf Source code
freq Man page Source code
generateHypothesis Source code
genewiseMult Source code
getConcordance Man page Source code
getLogFC Man page Source code
getMapping Source code
getMarginalHyperLikelihood Source code
getQRlm Source code
getQr Source code
getREvars Source code
getSSg_rNg Source code
getrc Man page Source code
getss Man page Source code
getwellKey Man page
getwellKey,SingleCellAssay-method Man page
getwss Man page Source code
glmDOF Source code
gseaAfterBoot Man page Source code
hushWarning Man page Source code
impute Man page Source code
influence.bayesglm Man page Source code
invlogit Man page Source code
listType Source code
logFC Man page Source code
logLik,GLMlike-method Man page
logLik,LMERlike-method Man page
logProd Source code
logit Source code
logmean Man page Source code
logshift Source code
lrTest Man page Source code
lrTest,LMlike,CoefficientHypothesis-method Man page
lrTest,LMlike,Hypothesis-method Man page
lrTest,LMlike,character-method Man page
lrTest,LMlike,matrix-method Man page
lrTest,ZlmFit,CoefficientHypothesis-method Man page
lrTest,ZlmFit,Hypothesis-method Man page
lrTest,ZlmFit,character-method Man page
lrTest,ZlmFit,matrix-method Man page
lrt Source code
lrtZlmFit Source code
lrtest Source code
maits Man page
makeChiSqTable Source code
makeContrastMatrixFromCoefficientHypothesis Source code
makeContrasts2 Source code
melt.SingleCellAssay Man page Source code
mkunique Source code
model.matrix Man page
model.matrix,LMlike-method Man page
model.matrix<- Man page
model.matrixBayes Source code
myBiplot Man page Source code
normalci Source code
nternalfilter Source code
numexp Man page Source code
orderCutpoints Source code
partialScore Man page Source code
pbootVcov1 Man page Source code
plot.thresholdSCRNACountMatrix Man page Source code
plotSCAConcordance Man page Source code
plotlrt Man page Source code
predict.ZlmFit Man page Source code
predict.bayesglm Source code
predictLM Source code
primerAverage Man page Source code
print.summaryThresholdSCRNA Man page Source code
print.summaryZlmFit Man page Source code
read.fluidigm Man page Source code
read.fluidigm.xls Source code
removeResponse Man page Source code
reraise Source code
residualsD Source code
residualsHook Source code
revealHook Source code
ridge.fit Source code
rotateMM Source code
rowm Source code
rstandard.bayesglm Man page Source code
safeCP Source code
safeContrastDP Source code
safeContrastQF Source code
se.coef Man page
se.coef,ZlmFit-method Man page
show,LMlike-method Man page
show,ZlmFit-method Man page
solveMoM Source code
split,SingleCellAssay,character-method Man page
split,SingleCellAssay,factor-method Man page
split,SingleCellAssay,list-method Man page
stat_ell Man page Source code
subset,SingleCellAssay-method Man page
summarize Man page
summary,GSEATests-method Man page
summary,LMlike-method Man page
summary,ZlmFit-method Man page
summary.thresholdSCRNACountMatrix Man page Source code
summary.zlm Source code
thresholdSCRNACountMatrix Man page Source code
toAdditiveFormula Source code
toAdditiveString Source code
torowm Source code
uncomplexify Source code
uniqueModNA Source code
uniqueModNA.old Source code
update,LMERlike-method Man page
update,LMlike-method Man page
vbeta Man page
vbetaFA Man page
vcov,GLMlike-method Man page
vcov,LMERlike-method Man page
vcov,ZlmFit-method Man page
waldTest Man page Source code
waldTest,LMlike,CoefficientHypothesis-method Man page
waldTest,LMlike,matrix-method Man page
waldTest,ZlmFit,CoefficientHypothesis-method Man page
waldTest,ZlmFit,Hypothesis-method Man page
waldTest,ZlmFit,matrix-method Man page
weights.default Source code
xform Man page Source code
zlm Man page Source code Source code
zlm.SingleCellAssay Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/Fluidigm-methods.R
R/GSEA-by-boot.R
R/Hypothesis.R
R/LmWrapper.R
R/MultidimensionalScaling.R
R/RNASeqAssay-methods.R
R/Readers.R
R/SingleCellAssay-methods.R
R/UtilityFunctions.R
R/ZlmFit-bootstrap.R
R/ZlmFit-logFC.R
R/ZlmFit.R
R/bayesglm.R
R/convertMASTClassic.R
R/ebayes-helpers.R
R/filterEval.R
R/helper-methods.R
R/lmWrapper-bayesglm.R
R/lmWrapper-glm.R
R/lmWrapper-glmer.R
R/lmWrapper-ridge.R
R/lrtest.R
R/predict.R
R/stat_ell.R
R/thresholdSCRNA.R
R/zeroinf.R
R/zlmHooks.R
README.md
_pkgdown.yml
build
build/vignette.rds
data
data/datalist
data/maits.RData
data/vbeta.RData
data/vbetaFA.RData
docs
docs/articles
docs/articles/MAITAnalysis.html
docs/articles/MAITAnalysis_cache
docs/articles/MAITAnalysis_cache/html
docs/articles/MAITAnalysis_files
docs/articles/MAITAnalysis_files/figure-html
docs/articles/MAST-intro.Rnw
docs/articles/MAST-intro.rel
docs/articles/figure
docs/articles/figure/advancedArmExample-1.pdf
docs/articles/figure/burdenOfFiltering-1.pdf
docs/articles/figure/splitbyncells-1.pdf
docs/articles/figure/tests-1.pdf
docs/articles/figure/zlmExample-1.pdf
docs/articles/framed.sty
docs/articles/index.html
docs/articles/symbols.tex
docs/authors.html
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/reference
docs/reference/BayesGLMlike-class.html
docs/reference/Drop.html
docs/reference/FromFlatDF.html
docs/reference/FromMatrix.html
docs/reference/GLMlike-class.html
docs/reference/GSEATests-class.html
docs/reference/Hypothesis.html
docs/reference/LMERlike-class.html
docs/reference/LMlike-class.html
docs/reference/LRT.html
docs/reference/MAST-package.html
docs/reference/ZlmFit-class.html
docs/reference/applyFlat.html
docs/reference/bootVcov1.html
docs/reference/cData.html
docs/reference/calcZ.html
docs/reference/colData-set-SingleCellAssay-DataFrame-method.html
docs/reference/collectResiduals.html
docs/reference/computeEtFromCt.html
docs/reference/condSd.html
docs/reference/condmean.html
docs/reference/convertMASTClassicToSingleCellAssay.html
docs/reference/defaultPrior.html
docs/reference/dof.html
docs/reference/ebayes.html
docs/reference/expavg.html
docs/reference/fData-methods.html
docs/reference/featureData-methods.html
docs/reference/filter-4.png
docs/reference/filter-6.png
docs/reference/filter.html
docs/reference/filterLowExpressedGenes.html
docs/reference/fit.html
docs/reference/freq.html
docs/reference/getConcordance.html
docs/reference/getwellKey.html
docs/reference/gseaAfterBoot.html
docs/reference/hushWarning.html
docs/reference/impute.html
docs/reference/index.html
docs/reference/influence.bayesglm.html
docs/reference/invlogit.html
docs/reference/logFC.html
docs/reference/logmean.html
docs/reference/lrTest-ZlmFit-character-method.html
docs/reference/lrTest.html
docs/reference/maits-dataset.html
docs/reference/melt.SingleCellAssay.html
docs/reference/model.matrix-set.html
docs/reference/model.matrix.html
docs/reference/myBiplot.html
docs/reference/numexp.html
docs/reference/pbootVcov1.html
docs/reference/plot.thresholdSCRNACountMatrix.html
docs/reference/plotSCAConcordance-7.png
docs/reference/plotSCAConcordance.html
docs/reference/plotlrt.html
docs/reference/predict.ZlmFit.html
docs/reference/primerAverage.html
docs/reference/print.summaryZlmFit.html
docs/reference/read.fluidigm.html
docs/reference/removeResponse.html
docs/reference/rstandard.bayesglm.html
docs/reference/se.coef.html
docs/reference/show.html
docs/reference/split-SingleCellAssay-character-method.html
docs/reference/stat_ell-6.png
docs/reference/stat_ell.html
docs/reference/subset-SingleCellAssay-method.html
docs/reference/summarize.html
docs/reference/summary-GSEATests-method.html
docs/reference/summary-ZlmFit-method.html
docs/reference/summary.thresholdSCRNACountMatrix.html
docs/reference/thresholdSCRNACountMatrix-13.png
docs/reference/thresholdSCRNACountMatrix.html
docs/reference/vbeta-dataset.html
docs/reference/vbetaFA-dataset.html
docs/reference/waldTest-ZlmFit-matrix-method.html
docs/reference/waldTest.html
docs/reference/xform.html
docs/reference/zlm.SingleCellAssay.html
docs/reference/zlm.html
inst
inst/NEWS
inst/doc
inst/doc/MAITAnalysis.R
inst/doc/MAITAnalysis.Rmd
inst/doc/MAITAnalysis.html
inst/doc/MAST-intro.R
inst/doc/MAST-intro.Rnw
inst/doc/MAST-intro.pdf
inst/extdata
inst/extdata/BTM_for_GSEA_20131008.gmt
man
man/BayesGLMlike-class.Rd
man/Drop.Rd
man/FromFlatDF.Rd
man/FromMatrix.Rd
man/GLMlike-class.Rd
man/GSEATests-class.Rd
man/Hypothesis.Rd
man/LMERlike-class.Rd
man/LMlike-class.Rd
man/LRT.Rd
man/MAST-package.Rd
man/ZlmFit-class.Rd
man/applyFlat.Rd
man/bootVcov1.Rd
man/cData.Rd
man/calcZ.Rd
man/colData-set-SingleCellAssay-DataFrame-method.Rd
man/collectResiduals.Rd
man/computeEtFromCt.Rd
man/convertMASTClassicToSingleCellAssay.Rd
man/defaultPrior.Rd
man/dof.Rd
man/ebayes.Rd
man/expavg.Rd
man/fData-methods.Rd
man/featureData-methods.Rd
man/filter.Rd
man/filterLowExpressedGenes.Rd
man/fit.Rd
man/freq.Rd
man/getConcordance.Rd
man/getwellKey.Rd
man/gseaAfterBoot.Rd
man/hushWarning.Rd
man/impute.Rd
man/influence.bayesglm.Rd
man/invlogit.Rd
man/logFC.Rd
man/logmean.Rd
man/lrTest-ZlmFit-character-method.Rd
man/lrTest.Rd
man/maits-dataset.Rd
man/melt.SingleCellAssay.Rd
man/model.matrix-set.Rd
man/model.matrix.Rd
man/myBiplot.Rd
man/pbootVcov1.Rd
man/plot.thresholdSCRNACountMatrix.Rd
man/plotSCAConcordance.Rd
man/plotlrt.Rd
man/predict.ZlmFit.Rd
man/primerAverage.Rd
man/print.summaryZlmFit.Rd
man/read.fluidigm.Rd
man/removeResponse.Rd
man/rstandard.bayesglm.Rd
man/se.coef.Rd
man/show.Rd
man/split-SingleCellAssay-character-method.Rd
man/stat_ell.Rd
man/subset-SingleCellAssay-method.Rd
man/summarize.Rd
man/summary-GSEATests-method.Rd
man/summary-ZlmFit-method.Rd
man/summary.thresholdSCRNACountMatrix.Rd
man/thresholdSCRNACountMatrix.Rd
man/vbeta-dataset.Rd
man/vbetaFA-dataset.Rd
man/waldTest-ZlmFit-matrix-method.Rd
man/waldTest.Rd
man/xform.Rd
man/zlm.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/SingleCellAssay-Object-MASTClassic.RData
tests/testthat/common-lmWrapper-glm-tests.R
tests/testthat/common-lmWrapper-tests.R
tests/testthat/helper-vbeta-init.R
tests/testthat/test-AllClasses.R
tests/testthat/test-FluidigmAssay.R
tests/testthat/test-GSEA-by-boot.R
tests/testthat/test-Hypothesis.R
tests/testthat/test-SingleCellAssay.R
tests/testthat/test-SummarizedExperiment.R
tests/testthat/test-bootstrap.R
tests/testthat/test-convertMASTClassic.R
tests/testthat/test-helper-methods.R
tests/testthat/test-lmWrapper-bayesglm.R
tests/testthat/test-lmWrapper-glm.R
tests/testthat/test-lmWrapper-glmer.R
tests/testthat/test-lrtest.R
tests/testthat/test-thresholding.R
tests/testthat/test-zeroinf.R
tests/testthat/test-zlmfit.R
vignettes
vignettes/MAITAnalysis.Rmd
vignettes/MAST-intro.Rnw
vignettes/symbols.tex
MAST documentation built on May 20, 2017, 10:16 p.m.