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