defunct {scran} | R Documentation

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`clusterSNNGraph` and `clusterKNNGraph` have been replaced by `clusterRows` with NNGraphParam or TwoStepParam from the bluster package.

`coassignProb` and `clusterRand` have been replaced by `pairwiseRand` from the bluster package.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

[Package scran version 1.22.1 Index]