FindParameters: Hyperparameter searching

In xnnba1984/DoubletCollection: Find doublets in scRNA-seq data

Hyperparameter searching

Description

Perform a grid search across user-specified hyperparameters. Return a combination of hyperparameters that optimize AUPRC or AUROC.

Usage

FindParameters(
  count,
  label,
  method,
  type,
  n_neighbors = NULL,
  min_gene_variability_pctl = NULL,
  n_prin_comps = NULL,
  nfeatures = NULL,
  PCs = NULL,
  nf = NULL,
  includePCs = NULL,
  max_depth = NULL,
  k = NULL,
  d = NULL,
  ntop.cxds = NULL,
  ntop.bcds = NULL,
  n_components = NULL,
  n_top_var_genes = NULL,
  n_iters = NULL
)

Arguments

count	A scRNA-seq count matrix.
label	A vector of doublet annotations.
method	A name of doublet-detection method.
type	"AUPRC" or "AUROC".
n_neighbors	Number of nearest neighbors in KNN classifier (Scrublet).
min_gene_variability_pctl	The top percentile of highly variable genes (Scrublet).
n_prin_comps	Number of principal components used to construct KNN classifer (Scrublet).
nfeatures	Number of highly variable genes (DoubletFinder).
PCs	Number of principal components used to construct KNN classifer (DoubletFinder).
nf	Number of highly variable genes (scDblFinder).
includePCs	Index of principal components to include in the predictors (scDblFinder).
max_depth	Maximum depth of decision trees (scDblFinder).
k	Number of nearest neighbors in KNN classifier (doubletCells).
d	Number of principal components used to construct KNN classifer (doubletCells).
ntop.cxds	Number of top variance genes to consider (cxds).
ntop.bcds	Number of top variance genes to consider (bcds).
n_components	Number of principal components used for clustering (DoubletDetection).
n_top_var_genes	Number of highest variance genes to use (DoubletDetection).
n_iters	Number of fit operations from which to collect p-values (DoubletDetection).

Value

A vector of hyperparameter combinations that maximize "AUPRC" or "AUROC".

Examples

data.list <- ReadData(path = ".../real_datasets")
count.list <- data.list$count
label.list <- lapply(data.list$label, FUN = function(label){
 ifelse(label == 'doublet', 1, 0)
})
count <- count.list$`pbmc-1A-dm`
label <- label.list$`pbmc-1A-dm`
result.parameter.scDblFinder <- FindParameters(count, label, method = 'scDblFinder', type = 'AUPRC',
nf=c(500, 1000, 1500, 2000, 2500),
includePCs=c(3, 4, 5, 6, 7),
max_depth=c(3, 4, 5, 6, 7))

xnnba1984/DoubletCollection documentation built on Dec. 10, 2022, 11:13 a.m.