R/seuratFunctions.R
runSeuratJackStraw.Rd
runSeuratJackStraw Compute jackstraw plot and store the computations in the input sce object
runSeuratJackStraw(
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 <- runSeuratNormalizeData(sce, useAssay = "counts")
sce <- runSeuratFindHVG(sce, useAssay = "counts")
sce <- runSeuratScaleData(sce, useAssay = "counts")
sce <- runSeuratPCA(sce, useAssay = "counts")
sce <- runSeuratJackStraw(sce, useAssay = "counts")
}