defunct: Defunct functions

In Alanocallaghan/scater: Single-Cell Analysis Toolkit for Gene Expression Data in R

Defunct functions

Description

Functions that have passed on to the function afterlife. Their successors are also listed.

Usage

calculateQCMetrics(...)

## S4 method for signature 'SingleCellExperiment'
normalize(object, ...)

centreSizeFactors(...)

calculateDiffusionMap(x, ...)

## S4 method for signature 'ANY'
calculateDiffusionMap(x, ...)

runDiffusionMap(...)

multiplot(...)

Arguments

object, x, ...

Ignored arguments.

Details

calculateQCMetrics is succeeded by perCellQCMetrics and perFeatureQCMetrics.

normalize is succeeded by logNormCounts.

centreSizeFactors has no replacement - the SingleCellExperiment is removing support for multiple size factors, so this function is now trivial.

runDiffusionMap and calculateDiffusionMap have no replacement. destiny is no longer on Bioconductor. You can calculate a diffusion map yourself, and add it to a reducedDim field, if you so wish.

Value

All functions error out with a defunct message pointing towards its descendent (if available).

Author(s)

Aaron Lun

Examples

try(calculateQCMetrics())

Alanocallaghan/scater documentation built on Feb. 10, 2024, 6:28 a.m.