Wrapper function to CisTarget parameters

Usage

params_cistarget(
  auc_threshold = 0.05,
  nes_threshold = 3,
  rcc_method = c("approx", "icistarget"),
  high_conf_cats = c("directAnnotation", "inferredBy_Orthology"),
  low_conf_cats = c("inferredBy_MotifSimilarity",
    "inferredBy_MotifSimilarity_n_Orthology")
)

Arguments

auc_threshold: Numeric between 0 and 1. Proportion of genes to use for AUC threshold calculation. Default is 0.05 (5% of genes).
nes_threshold: Numeric. Normalised Enrichment Score threshold for significant motifs. Default is 3.0.
rcc_method: Character. Method for recovery curve calculation. Either "approx" (approximate, faster) or "icistarget" (exact, slower).
high_conf_cats: Character vector. Annotation categories considered high confidence. Default includes direct annotations and orthology-based inferences.
low_conf_cats: Character vector. Annotation categories considered lower confidence. Default includes motif similarity-based inferences.

Value

A validated list of RcisTarget parameters.