ezcyclone: Cell cycle phase classification

In huipan1973/ezscrnaseq: What the Package Does (One Line, Title Case)

Cell cycle phase classification

Description

Cell cycle phase classification using scran cyclone.

Usage

ezcyclone(
  sce,
  organism = c("hsa", "mmu"),
  gene.names = NULL,
  pairs = NULL,
  ncores = 1,
  seed = 100,
  iter = 1000,
  min.iter = 100,
  min.pairs = 50,
  verbose = TRUE
)

Arguments

sce	A SingleCellExperiment object containing expression values, usually counts.
organism	hsa or mmu for human or mouse genes pre-trained marker sets.
gene.names	Ensembl gene IDs for genes in sce. length(gene.names) should match with nrow(sce).
pairs	Pair information for training marker sets. If set to NULL, uses pre-trained marker sets. Some genes in pairs should overlap with row.names(sce).
ncores	Number of cores.
seed	Random seed.
iter	An integer scalar specifying the number of iterations for random sampling to obtain a cycle score.
min.iter	An integer scalar specifying the minimum number of iterations for score estimation.
min.pairs	An integer scalar specifying the minimum number of pairs for cycle estimation.
verbose	TRUE/FASLE for specifying whether diagnostics should be printed to screen.

Value

A list containing phases, scores, and normalized.scores.

huipan1973/ezscrnaseq documentation built on July 12, 2022, 9:36 p.m.