tsneAUC: tsneAUC

In aertslab/SCENIC: SCENIC (Single Cell rEgulatory Network Inference and Clustering)

tsneAUC

Description

Calculates the t-SNE based on the regulon activity. (i.e. binary/continuous AUC)

Usage

tsneAUC(
  scenicOptions,
  aucType = NULL,
  nPcs = NULL,
  perpl = NULL,
  filePrefix = NULL,
  seed = NULL,
  onlyHighConf = FALSE,
  ...
)

Arguments

scenicOptions	Fields used:
aucType	"AUC" for continuous AUC, or "Binary" . By default it uses the value in getSettings(scenicOptions,"defaultTsne/dims")
nPcs	Number of PCs to use for the t-SNE (can be several values, see examples). By default it uses the value in getSettings(scenicOptions,"defaultTsne/dims")
perpl	Perplexity for the t-SNE (can be several values, see examples). By default it uses the value in getSettings(scenicOptions,"aucell/tsne_perpl")
filePrefix	Prefix for the file to save the t-SNE as. It is saved with the following format: "PREFIX_aucType_nPcs_perpl.Rds"
seed	Seed for the t-SNEs. By default it uses the value in getSettings(scenicOptions,"seed")
onlyHighConf	By default (TRUE) it only uses only regulons based on high-confidence annotations (i.e. "extended" are skipped)
...	Other arguments to pass to the Rtsne::Rtsne function.

Value

The file name(s) in whihc the tSNE is saved.

Examples

## TO DO (See the vignette)
# tSNE <- readRDS(tsneFileName(scenicOptions))
# tsneAUC(scenicOptions)

aertslab/SCENIC documentation built on April 7, 2024, 10 a.m.