Model-based Analysis of Single Cell Transcriptomics


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Documentation for package ‘MAST’ version 1.0.5

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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

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

-- A --

applyFlat Apply a vectorized binary operation recycling over last dimension

-- 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 Report the mean et value for each gene
condSd Report standard deviation of et, for positive et for each gene
continuous_residuals_hook Residual hooks and collection methods
convertMASTClassicToSingleCellAssay Convert a MASTClassic SingleCellAssay

-- D --

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 Report the proportion of expression for each gene
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 getConcordance
getLogFC Calculate log-fold changes from hurdle model components
getrc getConcordance
getss getConcordance
getwellKey Accessor for wellKey
getwellKey-method Accessor for wellKey
getwss getConcordance
GLMlike-class Wrapper for regular glm/lm
gseaAfterBoot Gene set analysis for hurdle model
GSEATests-class An S4 class for Gene Set Enrichment output

-- 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 --

maits MAITs data set, RNASeq
MAST MAST: Model-based Analysis of Single- cell Transcriptomics
melt.SingleCellAssay Melt a rectangular array
model.matrix Model matrix accessor
model.matrix-method Model matrix accessor
model.matrix<- Replace model matrix
myBiplot Makes a nice BiPlot

-- N --

numexp Report number of expressing cells per gene

-- 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 within duplicated genes/primers
print.summaryThresholdSCRNA Summarize the effect of thresholding
print.summaryZlmFit Print summary of a ZlmFit

-- R --

read.fluidigm read.fluidigm
removeResponse Remove the left hand side (response) from a formula
rstandard.bayesglm rstandard for bayesglm objects.

-- S --

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