SCENIC (version 1.1.2-01)

tsneAUC: 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

# NOT RUN {
## TO DO (See the vignette)
# tSNE <- readRDS(tsneFileName(scenicOptions))
# tsneAUC(scenicOptions)
# }