seuratComputeJackStraw {singleCellTK} | R Documentation

## seuratComputeJackStraw Compute jackstraw plot and store the computations in the input sce object

### Description

seuratComputeJackStraw Compute jackstraw plot and store the computations in the input sce object

### Usage

    seuratComputeJackStraw(
      inSCE,
      useAssay,
      dims = NULL,
      numReplicate = 100,
      propFreq = 0.025,
      externalReduction = NULL
    )

### Arguments

`inSCE` | (sce) object on which to compute and store jackstraw plot
`useAssay` | Assay containing scaled counts to use in JackStraw calculation.
`dims` | Number of components to test in Jackstraw. If `NULL`, then all components are used. Default `NULL`.
`numReplicate` | Numeric value indicating the number of replicate samplings to perform. Default value is `100`.
`propFreq` | Numeric value indicating the proportion of data to randomly permute for each replicate. Default value is `0.025`.
`externalReduction` | Pass DimReduc object if PCA/ICA computed through other libraries. Default `NULL`.

### Value

Updated `SingleCellExperiment` object with jackstraw computations stored in it

### Examples

    data(scExample, package = "singleCellTK")
    ## Not run:
    sce <- seuratNormalizeData(sce, useAssay = "counts")
    sce <- seuratFindHVG(sce, useAssay = "counts")
    sce <- seuratScaleData(sce, useAssay = "counts")
    sce <- seuratPCA(sce, useAssay = "counts")
    sce <- seuratComputeJackStraw(sce, useAssay = "counts")

    ## End(Not run)

[Package singleCellTK version 2.2.0 Index]