defunct: Defunct functions

In MarioniLab/scran: Methods for Single-Cell RNA-Seq Data Analysis

Defunct functions

Description

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

Usage

trendVar(...)

decomposeVar(...)

testVar(...)

improvedCV2(...)

technicalCV2(...)

makeTechTrend(...)

multiBlockVar(...)

multiBlockNorm(...)

overlapExprs(...)

parallelPCA(...)

bootstrapCluster(...)

clusterModularity(...)

clusterPurity(...)

clusterKNNGraph(...)

clusterSNNGraph(...)

coassignProb(...)

createClusterMST(...)

connectClusterMST(...)

orderClusterMST(...)

quickPseudotime(...)

testPseudotime(...)

doubletCells(...)

doubletCluster(...)

doubletRecovery(...)

Arguments

...	Ignored arguments.

Value

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

Variance modelling

trendVar, decomposeVar and testVar are succeeded by a suite of funtions related to modelGeneVar and fitTrendVar.

improvedCV2 and technicalCV2 are succeeded by modelGeneCV2 and fitTrendCV2.

makeTechTrend is succeeded by modelGeneVarByPoisson.

multiBlockVar is succeeded by the block argument in many of the modelling functions, and multiBlockNorm is no longer necessary.

Clustering-related functions

bootstrapCluster has been moved over to the bluster package, as the bootstrapStability function.

neighborsToSNNGraph and neighborsToKNNGraph have been moved over to the bluster package.

clusterModularity has been moved over to the bluster package, as the pairwiseModularity function.

clusterPurity has been moved over to the bluster package, as the neighborPurity function.

clusterSNNGraph and clusterKNNGraph have been replaced by clusterRows with NNGraphParam or TwoStepParam from the bluster package.

coassignProb and clusterRand have been replaced by pairwiseRand from the bluster package.

Pseudotime-related functions

createClusterMST, quickPseudotime and testPseudotime have been moved over to the TSCAN package.

connectClusterMST has been moved over to the TSCAN package, as the reportEdges function.

orderClusterMST has been moved over to the TSCAN package, as the orderCells function.

Doublet-related functions

doubletCells has been moved over to the scDblFinder package, as the computeDoubletDensity function.

doubletCluster has been moved over to the scDblFinder package, as the findDoubletClusters function.

doubletRecovery has been moved over to the scDblFinder package, as the recoverDoublets function.

Other functions

overlapExprs is succeeded by findMarkers with test.type="wilcox".

parallelPCA has been moved over to the PCAtools package.

Author(s)

Aaron Lun

Examples

try(trendVar())

MarioniLab/scran documentation built on Sept. 7, 2024, 6:25 a.m.