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