as.data.frame-methods: Converting BASiCS results objects to data.frames
In catavallejos/BASiCS: Bayesian Analysis of Single-Cell Sequencing data

as.data.frame,BASiCS_ResultsDE-method

R Documentation

Converting BASiCS results objects to data.frames

Description

Converting BASiCS results objects to data.frames

Usage

## S4 method for signature 'BASiCS_ResultsDE'
as.data.frame(x, Parameter, Filter = TRUE, ProbThreshold = NULL)

## S4 method for signature 'BASiCS_ResultDE'
as.data.frame(x, Filter = TRUE, ProbThreshold = NULL)

## S4 method for signature 'BASiCS_ResultVG'
as.data.frame(x, Filter = TRUE, ProbThreshold = NULL)

Arguments

`x`	An object of class BASiCS_ResultVG, BASiCS_ResultDE, or BASiCS_ResultsDE.
`Parameter`	For BASiCS_ResultsDE objects only. Character scalar specifying which table of results to output. Available options are "Mean", (mu, mean expression), "Disp" (delta, overdispersion) and "ResDisp" (epsilon, residual overdispersion).
`Filter`	Logical scalar. If `TRUE`, output only entries corresponding to genes that pass the decision rule used in the probabilistic test.
`ProbThreshold`	Only used if `Filter=TRUE`. Numeric scalar specifying the probability threshold to be used when filtering genes. Default is to use the threshold used in the original decision rule when the test was performed.