FindHVGs: Find high variable genes

In JiekaiLab/SOT: Single-cell Orientation Tracing

Description

Fing high variable genes by fitting a mean-dependent trend to the gene-specific variances.

Usage

FindHVGs(
  sce,
  datatype = "logcounts",
  genes.use = "filter.low",
  thr.bio = 0.5,
  thr.tech = NULL,
  thr.p.value = NULL,
  thr.FDR = NULL,
  thr.low = 0,
  thr.high = 20,
  show.plot = TRUE,
  ...
)

Arguments

sce	SingleCellExperiment object.
datatype	Sepcify the data type in sce to find hvgs.
genes.use	A logical vector in rowData to specify the genes for calculation.
thr.bio	The threshold of biological component of the variance.
thr.tech	The threshold of Technical component of the variance.
thr.p.value	The threshold of p-values for the test against the null hypothesis that bio=0.
thr.FDR	The threshold of adjusted p-values.
thr.low	The low threshold of mean log-expression.
thr.high	The high threshold of mean log-expression.
show.plot	Whether to plot the fitting results.
...	Additional arguments passed on to trendVar.

Value

SingleCellExperiment object with hvgs mask in rowData slot.

References

https://f1000research.com/articles/5-2122/v2

JiekaiLab/SOT documentation built on Jan. 25, 2022, 3:14 p.m.