Set PCA variances

Set PCA variances

pcaVariances(x, ...) <- value

Arguments

x

SCtkE object

...

other parameters

value

PCA variances DataFrame()

Value

A SCtkExperiment object with the pcaVariances slot set.

Examples

data("mouseBrainSubsetSCE")
pcaVariances(mouseBrainSubsetSCE)
#> DataFrame with 30 rows and 1 column
#>       percentVar
#>        <numeric>
#> PC1    0.3767783
#> PC2    0.0875963
#> PC3    0.0569427
#> PC4    0.0351618
#> PC5    0.0325555
#> ...          ...
#> PC26 1.15455e-02
#> PC27 1.04179e-02
#> PC28 9.64415e-03
#> PC29 8.95702e-03
#> PC30 7.43064e-32
#getPCA() sets the pcaVariances
newSCE <- getPCA(mouseBrainSubsetSCE, useAssay = "counts")

#alternatively, set the pcaVariances directly
pca <- prcomp(assay(mouseBrainSubsetSCE, "logcounts"))
percentVar <- pca$sdev ^ 2 / sum(pca$sdev ^ 2)
pcaVariances(mouseBrainSubsetSCE) <- DataFrame(percentVar)