MAST: Model-based Analysis of Single Cell Transcriptomics

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

Author
Andrew McDavid <Andrew_McDavid@urmc.rochester.edu>, Greg Finak <gfinak@fredhutch.org>, Masanao Yajima <myajima@fredhutch.org>
Date of publication
None
Maintainer
Andrew McDavid <Andrew_McDavid@urmc.rochester.edu>
License
GPL(>= 2)
Version
1.0.5
URLs

View on Bioconductor

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
condmean
Report the mean et value for each gene
condSd
Report standard deviation of et, for positive et for each...
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
Report the proportion of expression for each gene
FromFlatDF
Construct a SingleCellAssay (or derived subclass) from a...
FromMatrix
Construct a SingleCellAssay from a matrix or array of...
getConcordance
getConcordance
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 rectangular array
model.matrix
Model matrix accessor
model.matrix-set
Replace model matrix
myBiplot
Makes a nice BiPlot
numexp
Report number of expressing cells per gene
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 within duplicated genes/primers
print.summaryZlmFit
Print summary of a ZlmFit
read.fluidigm
read.fluidigm
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
Convenience function for running a zero-inflated regression
ZlmFit-class
An S4 class to hold the output of a call to zlm
zlm.SingleCellAssay
Zero-inflated regression for SingleCellAssay

Files in this package

MAST/DESCRIPTION
MAST/NAMESPACE
MAST/R
MAST/R/AllClasses.R
MAST/R/AllGenerics.R
MAST/R/Fluidigm-methods.R
MAST/R/GSEA-by-boot.R
MAST/R/Hypothesis.R
MAST/R/LmWrapper.R
MAST/R/MultidimensionalScaling.R
MAST/R/RNASeqAssay-methods.R
MAST/R/Readers.R
MAST/R/SingleCellAssay-methods.R
MAST/R/UtilityFunctions.R
MAST/R/ZlmFit-bootstrap.R
MAST/R/ZlmFit-logFC.R
MAST/R/ZlmFit.R
MAST/R/bayesglm.R
MAST/R/convertMASTClassic.R
MAST/R/ebayes-helpers.R
MAST/R/filterEval.R
MAST/R/helper-methods.R
MAST/R/lmWrapper-bayesglm.R
MAST/R/lmWrapper-glm.R
MAST/R/lmWrapper-glmer.R
MAST/R/lmWrapper-ridge.R
MAST/R/lrtest.R
MAST/R/predict.R
MAST/R/stat_ell.R
MAST/R/thresholdSCRNA.R
MAST/R/zeroinf.R
MAST/R/zlmHooks.R
MAST/README.md
MAST/build
MAST/build/vignette.rds
MAST/data
MAST/data/datalist
MAST/data/maits.RData
MAST/data/vbeta.RData
MAST/data/vbetaFA.RData
MAST/inst
MAST/inst/NEWS
MAST/inst/doc
MAST/inst/doc/MAITAnalysis.R
MAST/inst/doc/MAITAnalysis.Rmd
MAST/inst/doc/MAITAnalysis.html
MAST/inst/doc/MAST-intro.R
MAST/inst/doc/MAST-intro.Rnw
MAST/inst/doc/MAST-intro.pdf
MAST/inst/extdata
MAST/inst/extdata/BTM_for_GSEA_20131008.gmt
MAST/man
MAST/man/BayesGLMlike-class.Rd
MAST/man/Drop.Rd
MAST/man/FromFlatDF.Rd
MAST/man/FromMatrix.Rd
MAST/man/GLMlike-class.Rd
MAST/man/GSEATests-class.Rd
MAST/man/Hypothesis.Rd
MAST/man/LMERlike-class.Rd
MAST/man/LMlike-class.Rd
MAST/man/LRT.Rd
MAST/man/MAST-package.Rd
MAST/man/ZlmFit-class.Rd
MAST/man/applyFlat.Rd
MAST/man/bootVcov1.Rd
MAST/man/cData.Rd
MAST/man/calcZ.Rd
MAST/man/colData-set-SingleCellAssay-DataFrame-method.Rd
MAST/man/collectResiduals.Rd
MAST/man/computeEtFromCt.Rd
MAST/man/condSd.Rd
MAST/man/condmean.Rd
MAST/man/convertMASTClassicToSingleCellAssay.Rd
MAST/man/defaultPrior.Rd
MAST/man/dof.Rd
MAST/man/ebayes.Rd
MAST/man/expavg.Rd
MAST/man/fData-methods.Rd
MAST/man/featureData-methods.Rd
MAST/man/filter.Rd
MAST/man/filterLowExpressedGenes.Rd
MAST/man/fit.Rd
MAST/man/freq.Rd
MAST/man/getConcordance.Rd
MAST/man/getwellKey.Rd
MAST/man/gseaAfterBoot.Rd
MAST/man/hushWarning.Rd
MAST/man/impute.Rd
MAST/man/influence.bayesglm.Rd
MAST/man/invlogit.Rd
MAST/man/logFC.Rd
MAST/man/logmean.Rd
MAST/man/lrTest-ZlmFit-character-method.Rd
MAST/man/lrTest.Rd
MAST/man/maits-dataset.Rd
MAST/man/melt.SingleCellAssay.Rd
MAST/man/model.matrix-set.Rd
MAST/man/model.matrix.Rd
MAST/man/myBiplot.Rd
MAST/man/numexp.Rd
MAST/man/pbootVcov1.Rd
MAST/man/plot.thresholdSCRNACountMatrix.Rd
MAST/man/plotSCAConcordance.Rd
MAST/man/plotlrt.Rd
MAST/man/predict.ZlmFit.Rd
MAST/man/primerAverage.Rd
MAST/man/print.summaryZlmFit.Rd
MAST/man/read.fluidigm.Rd
MAST/man/removeResponse.Rd
MAST/man/rstandard.bayesglm.Rd
MAST/man/se.coef.Rd
MAST/man/show.Rd
MAST/man/split-SingleCellAssay-character-method.Rd
MAST/man/stat_ell.Rd
MAST/man/subset-SingleCellAssay-method.Rd
MAST/man/summarize.Rd
MAST/man/summary-GSEATests-method.Rd
MAST/man/summary-ZlmFit-method.Rd
MAST/man/summary.thresholdSCRNACountMatrix.Rd
MAST/man/thresholdSCRNACountMatrix.Rd
MAST/man/vbeta-dataset.Rd
MAST/man/vbetaFA-dataset.Rd
MAST/man/waldTest-ZlmFit-matrix-method.Rd
MAST/man/waldTest.Rd
MAST/man/xform.Rd
MAST/man/zlm.Rd
MAST/man/zlm.SingleCellAssay.Rd
MAST/tests
MAST/tests/testthat
MAST/tests/testthat.R
MAST/tests/testthat/SingleCellAssay-Object-MASTClassic.RData
MAST/tests/testthat/common-lmWrapper-glm-tests.R
MAST/tests/testthat/common-lmWrapper-tests.R
MAST/tests/testthat/helper-vbeta-init.R
MAST/tests/testthat/test-AllClasses.R
MAST/tests/testthat/test-FluidigmAssay.R
MAST/tests/testthat/test-GSEA-by-boot.R
MAST/tests/testthat/test-Hypothesis.R
MAST/tests/testthat/test-SingleCellAssay.R
MAST/tests/testthat/test-SummarizedExperiment.R
MAST/tests/testthat/test-bootstrap.R
MAST/tests/testthat/test-convertMASTClassic.R
MAST/tests/testthat/test-helper-methods.R
MAST/tests/testthat/test-lmWrapper-bayesglm.R
MAST/tests/testthat/test-lmWrapper-glm.R
MAST/tests/testthat/test-lmWrapper-glmer.R
MAST/tests/testthat/test-lrtest.R
MAST/tests/testthat/test-thresholding.R
MAST/tests/testthat/test-zeroinf.R
MAST/tests/testthat/test-zlmfit.R
MAST/vignettes
MAST/vignettes/MAITAnalysis.Rmd
MAST/vignettes/MAST-intro.Rnw
MAST/vignettes/symbols.tex