FindScores.All: Calculate doublet scores on multiple dataset

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

Calculate doublet scores on multiple dataset

Description

Call different computational doublet-detection methods to calculate doublet scores on multiple datasets.

Usage

FindScores.All(
  count.list,
  methods,
  n_neighbors = round(0.5 * sqrt(dim(count)[2])),
  min_gene_variability_pctl = 85L,
  n_prin_comps = 30L,
  nfeatures = 2000,
  PCs = 10,
  nf = 1000,
  includePCs = 5,
  max_depth = 5,
  k = 50,
  d = 50,
  ntop.cxds = 500,
  ntop.bcds = 500,
  n_components = 30,
  n_top_var_genes = 10000,
  n_iters = 5
)

Arguments

count.list	A list of scRNA-seq count matrix.
n_neighbors	The 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	The index of principal components to include in the predictors (scDblFinder).
max_depth	Maximum depth of decision trees (scDblFinder).
k	The 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).
method	A name vector of doublet-detection methods.

Value

A list of doublet scores calculated by each doublet-detection method on multiple datasets.

Examples

data.list <- ReadData(path = ".../real_datasets")
count.list <- data.list$count
methods <- c('Scrublet','doubletCells','cxds','bcds','hybrid','scDblFinder','DoubletDetection','DoubletFinder')
score.list.all <- FindScores.All(count.list, methods = methods)

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