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SingleCellAssay

Infrastructure and Tools for Single Cell Assay Analysis

Installation Instructions

 install.packages('devtools')
 library(devtools)
 install_github('SingleCellAssay', 'RGLab')
 # *or* if you don't have a working latex setup
 install_github('SingleCellAssay', 'RGLab', build_vignettes=FALSE)
 vignette('SingleCellAssay-intro')

Needs roxygen2 4.0.0.99 or higher (available on github) if the documentation is regenerated--otherwise the NAMESPACE file will not be correct.

Changes

New interface for zlm.SingleCellAssay to specify hypothesis. See ?Hypothesis API for zlm.SingleCellAssay has changed. Now a ZlmFit object is returned. Testing is done by calling waldTest or lrTest after the initial fit.

New Features

gseaAfterBoot for competitive geneset analysis under variance inflation
Support tests of arbitrary contrasts using LRT/zlm.SingleCellAssay

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Version

Version

0.925

License

Artistic-2.0

Maintainer

Last Published

December 22nd, 2017

Functions in PRIST (0.925)

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

DataLayer class

outlierDetection

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?

BayesGLMlike-class

Wrapper for bayesian GLM

SingleCellAssay-package

"Tools for Single Cell Assay Analysis"

SingleCellAssay

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

burdenOfFiltering

Burden of filtering

combine,SingleCellAssay,SingleCellAssay-method

Combine two SingleCellAssay or derived classes

combined_residuals_hook

Hook to get the combined residuals

Degrees of freedom of Zero inflated model

Estimate hyperparameters for hierarchical variance model for continuous component

fit,LMERlike,missing-method

fit a zero-inflated regression

Gene set analysis for hurdle model

Get name of active layer

length,SCASet-method

Get the length of an SCASet

NanoStringAssay

NanoString Assay Constructor

RNASeqAssay-class

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

deviance_residuals_hook

Standardized deviance residuals hook

discrete_residuals_hook

hHook to get the continuous residuals

Filter a SingleCellAssay

filterLowExpressedGenes

Filter low-expressing genes

Report the proportion of expression for each gene

Which layer is active?

Set name of active layer

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.bayesglm

rstandard for bayesglm objects.

Constructs a SCASet

SingleCellAssay-class

SingleCellAssay class

Accessor for cellData data.frame

Get Z or T statistics and P values after running gseaAfterBoot

computeEtFromCt

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

[[<-,DataLayer-method

Replace a section of a DataLayer

influence.bayesglm

influence for bayesglm objects.

lapply,SCASet-method

Apply a function to each member of a SCASet

Set active layer

Exponential average

exprs,DataLayer-method

Get or set a matrix of measurement values in a SingleCellAssay

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

melt.SingleCellAssay

mergeWithKeyFile

Merge NanoString lanes with a key file

plotSCAConcordance

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

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

readNanoStringLanes

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

Hook to compute the combined residuals with treatment effects added back.

[[,DataLayer-method

Extract from a DataLayer

[[,SCASet-method

Index into an SCASet object

print.summaryZlmFit

Print summary of a ZlmFit

show,Mapping-method

split,DataLayer-method

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

zlm.SingleCellAssay

Zero-inflated regression for SingleCellAssay

Vbeta Data Set, FluidigmAssay

thresholdNanoString,NanoStringAssay-method

Estimate thresholds for positive expression

thresholdNanoString

thresholds for positive expression

Variance-covariance matrix for zero inflated

waldTest,ZlmFit,matrix-method