Model-based Analysis of Single Cell Transcriptomics

Documentation for package ‘MAST’ version 1.25.1

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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: Model-based Analysis of Single- cell Transcriptomics

-- A --

applyFlat	Apply a vectorized binary operation recycling over last dimension
assay-method	Default 'assay' returned
assay_idx	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	Defunct functions in package 'MAST'
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
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
CovFromBoots	Extract the inter-gene covariance matrices for continuous and discrete components of a MAST model for a given coefficient from bootstrap replicates

-- 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
exprs	Defunct functions in package 'MAST'

-- F --

fData	Defunct functions in package 'MAST'
filter	Defunct functions in package 'MAST'
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-defunct	Defunct functions in package 'MAST'
mast_filter	Filter a SingleCellAssay
meld_list_left	Combine lists, preferentially taking elements from x if there are duplicate names
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 --

new_with_repaired_slots	Instantiate a class, but warn rather than error for badly named slots
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.
predicted_sig	Predicted signatures
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
"summary.ZlmFit"	Summarize model features from a 'ZlmFit' object
"ZlmFit-summary",	Summarize model features from a 'ZlmFit' object