Loading, transforming and summarizing

Functions to load data, add covariates or annotations, or provide high-level summaries.

Convert a MASTClassic SingleCellAssay

Filter a SingleCellAssay

Summary statistics for genes in an experiment

Construct a SingleCellAssay (or derived subclass) from a `flat` (melted) data.frame/data.table

Construct a SingleCellAssay from a matrix or array of expression

Get the concordance between two experiments

"Melt" a

Average expression values for duplicated/redundant genes

Reads a Fluidigm Biomark (c. 2011) raw data file (or set of files)

Zero-inflated regression for SingleCellAssay

Thresholding

Adaptive thresholding of background noise.

Plot cutpoints and densities for thresholding

Summarize the effect of thresholding

Threshold a count matrix using an adaptive threshold.

Differential Expression Testing with Hurdle Model

Fit a Hurdle linear model to test for zero-inflated differential expression.

Wrapper for bayesian GLM

Initialize a prior to be used a prior for BayeGLMlike/BayesGLMlike2

Estimate hyperparameters for hierarchical variance model for continuous component

Wrapper for lmer/glmer

Print summary of a ZlmFit

Zero-inflated regression for SingleCellAssay

Specifying hypothesis and contrasts to test

Testing linear functions of coefficients.

Describe a linear model hypothesis to be tested

Run a likelihood-ratio test

Run a Wald test

Low-level manipulation of fitted hurdle models

Return coefficients, standard errors, etc. Calculate and return residuals from models.

Residual hooks and collection methods

impute missing continuous expression for plotting

Calculate log-fold changes from hurdle model components

Return predictions from a ZlmFit object.

Return coefficient standard errors

An S4 class to hold the output of a call to zlm

Gene set enrichment testing

Tests on the average differential expression effect in a gene set, accounting for gene-gene correlations. Uses bootstraps to assess the gene-gene correlations.

Bootstrap a zlmfit

Gene set analysis for hurdle model

Bootstrap a zlmfit

Summarize gene set enrichment tests

Plotting methods

Miscellaneous plotting methods. Concordance, PCA biplots, and effects plots for fitted hurdle models.

Makes a nice BiPlot

Concordance plots of filtered single vs n-cell assays

Plot confidence ellipse in 2D