perform.PCA — perform.PCA • DEprot

This function performs principal component analyses (PCA).

perform.PCA(
  DEprot.object,
  sample.subset = NULL,
  which.data = "imputed",
  n.PCs = 50,
  center.data = TRUE,
  scale.data = TRUE
)

Arguments

DEprot.object: An object of class DEprot or DEprot.analyses.
sample.subset: String vector indicating the column names (samples) to keep in the counts table (the 'column.id' in the metadata table). Default: NULL (no subsetting).
which.data: String indicating which type of counts should be used. One among: 'raw', 'normalized', 'norm', 'imputed', 'imp'. Default: "imputed".
n.PCs: Integer number indicating the number of PCs to be computed. This is used only when NAs are present in the the data set. Default: 50.
center.data: Logical value indicating whether the data should be centered. Default: TRUE.
scale.data: Logical value indicating whether the data should be scaled. Default: TRUE.

A DEprot.PCA, containing the PC values (PCs) and the importance summary (importance).

Sebastian Gregoricchio

pca <- perform.PCA(DEprot.object = DEprot::test.toolbox$dpo.imp)