getICAGenes: Get significant ICA genes

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Get significant ICA genes

Description

Given feature loadings obtained from independent component analysis (ICA), significant genes for each component are identified.

Usage

getICAGenes(
  feature.loading,
  fdr.cutoff = 1e-04,
  local.fdr = T,
  assert.positive.skew = T,
  only.pos = T
)

Arguments

feature.loading	ICA feature loadings
fdr.cutoff	FDR threshold. Default is 0.0001.
local.fdr	Whether to use local FDR. Default is T.
assert.positive.skew	Whether to ensure that max(|feature.loading|) is positive. Default is T.
only.pos	Whether significant genes are positively loaded only. Default is T.

Value

named list of ICA gene programs

Author(s)

Nicholas Mikolajewicz

References

https://nmikolajewicz.github.io/scMiko/articles/Module_Detection.html

See Also

runICA for independent component analysis.

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.