Drop specified dimension from an array
Constructor for a FluidigmAssay
Linear Model-like Class
Likelihood Ratio Tests for SingleCellAssays
Describe a linear model hypothesis to be tested
Wrapper for lmer/glmer
Construct a SingleCellAssay from a matrix or array of expression
Wrapper for regular glm/lm
Wrapper for bayesian GLM
DataLayer class
SingleCellAssay: A constructor for an object of type SingleCellAssay.
ThresholdedNanoString-class
Holds output and diagnostics from thresholdNanoString
Not intended to be called by the user.
Apply a vectorized binary operation recycling over last dimension
Bootstrap a zlmfit
Report standard deviation of et, for positive et for each gene
Report the mean et value for each gene
RNASeqAssay class. Doesn't require ncells
Filter an RNASeqAssay
combine,SingleCellAssay,ANY-method
Combine a SingleCellAssay and a vector, data.frame or AnnotatedDataFrame
SingleCellAssay class
"Tools for Single Cell Assay Analysis"
Coefficients of zero-inflated
SCASet is a set of SingleCellAssay objects or objects of its subclasses (i.e. FluidigmAssay)
The constructor SCASet
should be used to make objects of this class.
Get Z or T statistics and P values after running gseaAfterBoot
Accessor for cellData AnnotatedDataFrame
combine,SCASet,missing-method
Combines a SCASet into a unified SingleCellAssay
Initialize a prior to be used a prior for BayeGLMlike/BayesGLMlike2
Standardized deviance residuals hook
Estimate hyperparameters for hierarchical variance model for continuous component
Exponential average
getss
Constructs a SCASet
Do two objects conform in dimension and type?
continuous_residuals_hook
Hook to get the discrete residuals
Filter low-expressing genes
fit a zero-inflated regression
Report the proportion of expression for each gene
getConcordance
An S4 class to hold the output of a call to zlm
Layer management methods
Burden of filtering
combine,SingleCellAssay,SingleCellAssay-method
Combine two SingleCellAssay or derived classes
Hook to get the combined residuals
computeEtFromCt
Get or set a matrix of measurement values in a SingleCellAssay
fData
Selectively muffle warnings based on output
fit,LMERlike,missing-method
##'
getwss
Gene set analysis for hurdle model
getrc
Calculate log-fold changes from hurdle model components
Log mean
Accessor for cellData data.frame
hHook to get the continuous residuals
Degrees of freedom of Zero inflated model
Accessor for wellKey
Which layer is active?
Set name of active layer
influence for bayesglm objects.
Get name of active layer
Get the length of an SCASet
Concordance plots of filtered single vs n-cell assays
Plot a likelihood ratio test object
split,SingleCellAssay-method
Split into SCASet
Model matrix accessor
Makes a nice BiPlot
sampleNames,SCASet-method
get the sample names in an SCASet
Hook to compute the combined residuals with treatment effects added back.
How many layers does a DataLayer have?
Report number of expressing cells per gene
read.fluidigm
lrTest,ZlmFit,character-method
Likelihood ratio test
Run a likelihood-ratio test
Bootstrap a zlmfit
plot.thresholdSCRNACountMatrix
Plot cutpoints and densities for thresholding
Show methods
Split a DataLayer correctly
Summarize model features from a ZlmFit
object
Return a human-readable summary
Run a Wald test
Make matrix of continuous expression values, orthogonal to discrete
Accessor for featureData AnnotatedDataFrame
Filter a SingleCellAssay
Apply a function to each member of a SCASet
rstandard for bayesglm objects.
Replace a section of a DataLayer
Subset a SingleCellAssay by data in cellData
[,DataLayer,ANY,ANY-method
Subset a DataLayer
Extract from a DataLayer
Index into an SCASet object
Set active layer
Melt a rectangular array
Replace model matrix
summary.thresholdSCRNACountMatrix
Summarize the effect of thresholding
thresholds for positive expression
Convenience function for running a zero-inflated regression
Zero-inflated regression for SingleCellAssay
Subset an SCASet to a smaller SCASet
[,SingleCellAssay,ANY,ANY-method
Subset a SingleCellAssay
Variance-covariance matrix for zero inflated
Vbeta Data Set
Vbeta Data Set, FluidigmAssay
waldTest,ZlmFit,matrix-method
Wald test
Average within duplicated genes/primers
Print summary of a ZlmFit
Used to compute module "scores"
Hook to return p_hat from the model
Return programmatically useful summary of a fit
summary,SingleCellAssay-method
Summarize expression parameters
thresholdSCRNACountMatrix
Threshold a count matrix using an adaptive threshold.
Convert a pair of character names to a list that can be placed into a data.table