size_factors: Calculate deconvolving size factors from cell pools

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

Calculate deconvolving size factors from cell pools

Description

Calculate deconvolving size factors from cell pools using scran computeSumFactors

Usage

size_factors(
  sce,
  min.size = 10,
  max.size = 3000,
  min.mean = 0.1,
  method = "igraph",
  group.col = NULL,
  seed = 100,
  ncores = 1,
  prefix = NULL,
  plot = TRUE,
  verbose = TRUE
)

Arguments

sce	A SingleCellExperiment object containing expression values, usually counts.
min.size	An integer scalar specifying the minimum size of each cluster.
max.size	Maximum cluster size.
min.mean	A numeric scalar specifying the filter to be applied on the average count for each filter prior to computing ranks. Only used when use.ranks=TRUE, see ?scaledColRanks for details.
method	String specifying the clustering method to use. "hclust" uses hierarchical clustering while "igraph" uses graph-based clustering.
group.col	column name of the groups.
seed	Random seed.
ncores	Number of cores.
prefix	Prefix for file name for the QC metrics histograms.
plot	TRUE/FASLE for whether plot the QC metrics histograms.
verbose	TRUE/FASLE for specifying whether diagnostics should be printed to screen.

Value

A SingleCellExperiment object with size factors.

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