MAST: Model-based Analysis of Single Cell Transcriptomics

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

AuthorAndrew McDavid <Andrew_McDavid@urmc.rochester.edu>, Greg Finak <gfinak@fredhutch.org>, Masanao Yajima <myajima@fredhutch.org>
Date of publicationNone
MaintainerAndrew McDavid <Andrew_McDavid@urmc.rochester.edu>
LicenseGPL(>= 2)
Version1.0.5
https://github.com/RGLab/MAST/

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

Functions

applyFlat Man page
BayesGLMlike-class Man page
bootVcov1 Man page
burdenOfFiltering Man page
calcZ Man page
cData Man page
cData<- Man page
cData<-,SingleCellAssay-method Man page
cData,SingleCellAssay-method Man page
CoefficientHypothesis Man page
coef,LMERlike-method Man page
coef,ZlmFit-method Man page
colData<-,SingleCellAssay,DataFrame-method Man page
collectResiduals Man page
combined_residuals_hook Man page
combine,SingleCellAssay,ANY-method Man page
combine,SingleCellAssay,SingleCellAssay-method Man page
computeEtFromCt Man page
condmean Man page
condSd Man page
continuous_residuals_hook Man page
convertMASTClassicToSingleCellAssay Man page
defaultPrior Man page
deviance_residuals_hook Man page
discrete_residuals_hook Man page
dof Man page
dof,GLMlike-method Man page
Drop Man page
ebayes Man page
expavg Man page
fData Man page
fData,SingleCellAssay-method Man page
featureData Man page
featureData,SingleCellAssay-method Man page
filter Man page
filterLowExpressedGenes Man page
fit Man page
fit,GLMlike,missing-method Man page
fit,LMERlike,missing-method Man page
fitted_phat Man page
FluidigmAssay Man page
freq Man page
FromFlatDF Man page
FromMatrix Man page
getConcordance Man page
getLogFC Man page
getrc Man page
getss Man page
getwellKey Man page
getwellKey,SingleCellAssay-method Man page
getwss Man page
GLMlike-class Man page
gseaAfterBoot Man page
GSEATests-class Man page
hushWarning Man page
Hypothesis Man page
impute Man page
influence.bayesglm Man page
invlogit Man page
LMERlike-class Man page
LMlike-class Man page
logFC Man page
logLik,GLMlike-method Man page
logLik,LMERlike-method Man page
logmean Man page
LRT Man page
lrTest Man page
lrTest,LMlike,character-method Man page
lrTest,LMlike,CoefficientHypothesis-method Man page
lrTest,LMlike,Hypothesis-method Man page
lrTest,LMlike,matrix-method Man page
lrTest,ZlmFit,character-method Man page
lrTest,ZlmFit,CoefficientHypothesis-method Man page
lrTest,ZlmFit,Hypothesis-method Man page
lrTest,ZlmFit,matrix-method Man page
LRT,SingleCellAssay,character-method Man page
maits Man page
MAST Man page
MAST-package Man page
melt.SingleCellAssay Man page
model.matrix Man page
model.matrix<- Man page
model.matrix,LMlike-method Man page
myBiplot Man page
numexp Man page
partialScore Man page
pbootVcov1 Man page
plotlrt Man page
plotSCAConcordance Man page
plot.thresholdSCRNACountMatrix Man page
predict.ZlmFit Man page
primerAverage Man page
print.summaryThresholdSCRNA Man page
print.summaryZlmFit Man page
read.fluidigm Man page
removeResponse Man page
rstandard.bayesglm Man page
se.coef Man page
se.coef,ZlmFit-method Man page
show,LMlike-method Man page
show,ZlmFit-method Man page
SingleCellAssay Man page
split,SingleCellAssay,character-method Man page
split,SingleCellAssay,factor-method Man page
split,SingleCellAssay,list-method Man page
stat_ell Man page
subset,SingleCellAssay-method Man page
summarize Man page
summary,GSEATests-method Man page
summary,LMlike-method Man page
summary.thresholdSCRNACountMatrix Man page
summary,ZlmFit-method Man page
thresholdSCRNACountMatrix Man page
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
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
xform Man page
zlm Man page
ZlmFit-class Man page
zlm.SingleCellAssay Man page

Files

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

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