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
Specify name of the assay to use for scaling. Assay name
provided against this parameter is scaled by the function and used
for the computation of JackStraw scores along with the reduced dimensions
specified by the dims
parameter.
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")
}