Cepo: Computing Cepo cell identity genes

In PYangLab/Cepo: Cepo for the identification of differentially stable genes

Computing Cepo cell identity genes

Description

ExprsMat accepts various matrix objects, including DelayedArray and HDF5Array for out-of-memory computations. See vignette.

Usage

Cepo(
  exprsMat,
  cellTypes,
  minCells = 20,
  minCelltype = 3,
  exprsPct = 0.05,
  prefilter_sd = NULL,
  prefilter_pzero = NULL,
  logfc = NULL,
  computePvalue = NULL,
  computeFastPvalue = TRUE,
  variability = "CV",
  method = "weightedMean",
  weight = c(0.5, 0.5),
  workers = 1L,
  block = NULL,
  ...
)

Arguments

exprsMat	Expression matrix where columns denote cells and rows denote genes
cellTypes	Vector of cell type labels
minCells	Integer indicating the minimum number of cells required within a cell type
minCelltype	Integer indicating the minimum number of cell types required in each batch
exprsPct	Percentage of lowly expressed genes to remove. Default to NULL to not remove any genes.
prefilter_sd	Numeric value indicating threshold relating to standard deviation of genes. Used with prefilter_zeros.
prefilter_pzero	Numeric value indicating threshold relating to the percentage of zero expression of genes. Used with prefilter_sd.
logfc	Numeric value indicating the threshold of log fold-change to use to filter genes.
computePvalue	Whether to compute p-values using bootstrap test. Default to NULL to not make computations. Set this to an integer to set the number of bootstraps needed (recommend to be at least 100).
computeFastPvalue	Logical vector indicating whether to perform a faster version of p-value calculation. Set to TRUE by default.
variability	A character indicating the stability measure (CV, IQR, MAD, SD). Default is set to CV.
method	Character indicating the method for integration the two stability measures. By default this is set to 'weightedMean' with equal weights.
weight	Vector of two values indicating the weights for each stability measure. By default this value is c(0.5, 0.5).
workers	Number of cores to use. Default to 1, which invokes BiocParallel::SerialParam. For workers greater than 1, see the workers argument in BiocParallel::MulticoreParam and BiocParallel::SnowParam.
block	Vector of batch labels
...	Additional arguments passed to BiocParallel::MulticoreParam and BiocParallel::SnowParam.

Value

Returns a list of key genes.

Examples

library(SingleCellExperiment)
data('cellbench', package = 'Cepo')
cellbench
cepoOutput <- Cepo(logcounts(cellbench), cellbench$celltype)
cepoOutput

PYangLab/Cepo documentation built on June 29, 2024, 7:16 p.m.