R/seuratFunctions.R
seuratComputeJackStraw.Rd
seuratComputeJackStraw Compute jackstraw plot and store the computations in the input sce object
seuratComputeJackStraw( inSCE, useAssay, dims = NULL, numReplicate = 100, propFreq = 0.025, externalReduction = NULL )
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 |
numReplicate | Numeric value indicating the number of replicate
samplings to perform.
Default value is |
propFreq | Numeric value indicating the proportion of data to randomly
permute for each replicate.
Default value is |
externalReduction | Pass DimReduc object if PCA/ICA computed through
other libraries. Default |
Updated SingleCellExperiment
object with jackstraw
computations stored in it
data(scExample, package = "singleCellTK") if (FALSE) { 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") }