Model-based Analysis of Single Cell Transcriptomics


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Documentation for package ‘MAST’ version 1.8.2

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A B C D E F G H I L M N P R S T U V W X Z misc

MAST-package MAST: Model-based Analysis of Single- cell Transcriptomics

-- A --

applyFlat Apply a vectorized binary operation recycling over last dimension
assay-method Default 'assay' returned

-- B --

BayesGLMlike-class Wrapper for bayesian GLM
bootVcov1 Bootstrap a zlmfit
burdenOfFiltering Filter a SingleCellAssay

-- C --

calcZ Get Z or T statistics and P values after running gseaAfterBoot
cData Deprecated cell/feature data accessors/mutators
cData-method Deprecated cell/feature data accessors/mutators
cData<- Deprecated cell/feature data accessors/mutators
cData<--method Deprecated cell/feature data accessors/mutators
coef-method Wrapper for lmer/glmer
coef-method An S4 class to hold the output of a call to zlm
CoefficientHypothesis Describe a linear model hypothesis to be tested
colData<--method Replace 'colData'
collectResiduals Residual hooks and collection methods
combine-method Deprecated cell/feature data accessors/mutators
combined_residuals_hook Residual hooks and collection methods
computeEtFromCt Compute the Et from the Ct
condmean Summary statistics for genes in an experiment
condSd Summary statistics for genes in an experiment
continuous_residuals_hook Residual hooks and collection methods
convertMASTClassicToSingleCellAssay Convert a MASTClassic SingleCellAssay

-- D --

defaultAssay Default 'assay' returned
defaultPrior Initialize a prior to be used a prior for BayeGLMlike/BayesGLMlike2
deviance_residuals_hook Residual hooks and collection methods
discrete_residuals_hook Residual hooks and collection methods
dof Degrees of freedom of Zero inflated model
dof-method Degrees of freedom of Zero inflated model
Drop Drop specified dimension from an array

-- E --

ebayes Estimate hyperparameters for hierarchical variance model for continuous component
expavg Exponential average

-- F --

fData fData
fData-method fData
featureData Accessor for featureData 'AnnotatedDataFrame'
featureData-method Accessor for featureData 'AnnotatedDataFrame'
filter Filter a SingleCellAssay
filterLowExpressedGenes Filter low-expressing genes
fit fit a zero-inflated regression
fit-method fit a zero-inflated regression
fitted_phat Residual hooks and collection methods
FluidigmAssay Construct a SingleCellAssay (or derived subclass) from a 'flat' (melted) data.frame/data.table
freq Summary statistics for genes in an experiment
FromFlatDF Construct a SingleCellAssay (or derived subclass) from a 'flat' (melted) data.frame/data.table
FromMatrix Construct a SingleCellAssay from a matrix or array of expression

-- G --

getConcordance Get the concordance between two experiments
getLogFC Calculate log-fold changes from hurdle model components
getrc Get the concordance between two experiments
getss Get the concordance between two experiments
getwellKey Accessor for wellKey
getwellKey-method Accessor for wellKey
getwss Get the concordance between two experiments
GLMlike-class Wrapper for regular glm/lm
gseaAfterBoot Gene set analysis for hurdle model
GSEATests-class An S4 class for Gene Set Enrichment output
gsea_control Gene set analysis for hurdle model

-- H --

hushWarning Selectively muffle warnings based on output
Hypothesis Describe a linear model hypothesis to be tested

-- I --

impute impute missing continuous expression for plotting
influence.bayesglm Influence bayesglm object
invlogit Inverse of logistic transformation

-- L --

LMERlike-class Wrapper for lmer/glmer
LMlike-class Linear Model-like Class
logFC Calculate log-fold changes from hurdle model components
logLik-method Wrapper for lmer/glmer
logLik-method Linear Model-like Class
logmean Log mean
LRT Likelihood Ratio Tests for SingleCellAssays
LRT-method Likelihood Ratio Tests for SingleCellAssays
lrTest Run a likelihood-ratio test
lrTest-method Linear Model-like Class
lrTest-method An S4 class to hold the output of a call to zlm
lrTest-method Likelihood ratio test

-- M --

magic_assay_names Default 'assay' returned
maits MAITs data set, RNASeq
MAST MAST: Model-based Analysis of Single- cell Transcriptomics
mast_filter Filter a SingleCellAssay
melt.SingleCellAssay "Melt" a 'SingleCellAssay' matrix
model.matrix Model matrix accessor
model.matrix-method Model matrix accessor
model.matrix<- Replace model matrix
myBiplot Makes a nice BiPlot

-- N --

numexp Summary statistics for genes in an experiment

-- P --

partialScore Residual hooks and collection methods
pbootVcov1 Bootstrap a zlmfit
plot.thresholdSCRNACountMatrix Plot cutpoints and densities for thresholding
plotlrt Plot a likelihood ratio test object
plotSCAConcordance Concordance plots of filtered single vs n-cell assays
predict.ZlmFit Return predictions from a ZlmFit object.
primerAverage Average expression values for duplicated/redundant genes
print.summaryThresholdSCRNA Summarize the effect of thresholding
print.summaryZlmFit Print summary of a ZlmFit

-- R --

read.fluidigm Reads a Fluidigm Biomark (c. 2011) raw data file (or set of files)
removeResponse Remove the left hand side (response) from a formula
rstandard.bayesglm rstandard for bayesglm objects.

-- S --

SceToSingleCellAssay Coerce a SingleCellExperiment to some class defined in MAST
se.coef Return coefficient standard errors
se.coef-method An S4 class to hold the output of a call to zlm
show-method show
SingleCellAssay Construct a SingleCellAssay (or derived subclass) from a 'flat' (melted) data.frame/data.table
split-method Split into 'list'
stat_ell Plot confidence ellipse in 2D
subset-method Subset a 'SingleCellAssay' by cells (columns)
summarize Return programmatically useful summary of a fit
summary-method Linear Model-like Class
summary-method Summarize gene set enrichment tests
summary-method Summarize model features from a 'ZlmFit' object
summary.thresholdSCRNACountMatrix Summarize the effect of thresholding

-- T --

thresholdSCRNACountMatrix Threshold a count matrix using an adaptive threshold.

-- U --

update-method Wrapper for lmer/glmer
update-method Linear Model-like Class

-- V --

vbeta Vbeta Data Set
vbetaFA Vbeta Data Set, FluidigmAssay
vcov-method Wrapper for regular glm/lm
vcov-method Wrapper for lmer/glmer
vcov-method An S4 class to hold the output of a call to zlm

-- W --

waldTest Run a Wald test
waldTest-method Linear Model-like Class
waldTest-method An S4 class to hold the output of a call to zlm
waldTest-method Wald test

-- X --

xform Make matrix of continuous expression values, orthogonal to discrete

-- Z --

zlm Zero-inflated regression for SingleCellAssay
zlm.SingleCellAssay Zero-inflated regression for SingleCellAssay
ZlmFit An S4 class to hold the output of a call to zlm
ZlmFit-class An S4 class to hold the output of a call to zlm

-- misc --

"summary-ZlmFit", Summarize model features from a 'ZlmFit' object
"ZlmFit-summary" Summarize model features from a 'ZlmFit' object