runNMF: Perform non-negative matrix factorization (NMF)

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

Perform non-negative matrix factorization (NMF)

Description

Run non-negative matrix factorization(NMF or NNMF) using sequential coordinate-wise descent or multiplicative updates on Seurat object.

Usage

runNMF(
  object,
  assay = DefaultAssay(object),
  k = 6,
  raster = F,
  n.threads = 2,
  features = NULL,
  feature.min.pct = 0,
  max.iter = 50,
  gene.cutoff = 0.5,
  gene.n = 50,
  reduction = "umap",
  sample.name = NULL,
  show.top.n = 10,
  pathway.db = "Bader",
  do.enrichment = T,
  verbose = T,
  ...
)

Arguments

object	Seurat object
assay	assay. Default is DefaultAssay(object).
k	Number of NMF gene programs Default is 6.
raster	rasterize output plot. Default is F.
n.threads	Number of threads to use when running NMF. Default is 2.
features	features to run NMF on.
feature.min.pct	minimum expressing fraction for feature to run NMF on. Default is 0. Ignored if 'features' are specified.
max.iter	Maximum iteration of alternating NNLS solutions to H and W
gene.cutoff	Feature loading cutoff threshold [0,1]. Default = 0.5. Ignored if gene.n is specified.
gene.n	number of genes to return per gene program
reduction	reduction used for visualizing gene program expression. Default is "umap".
sample.name	sample name. Default is NULL.
show.top.n	number of enrichment terms to show in summary plots. Ignoried if do.enrichment = F.
pathway.db	pathway database to use for enrichment analysis. Options are "GO" or "Bader". Default is "Bader". Ignored if do.enrichment = F.
do.enrichment	Whether to run enrichment analysis.
verbose	Print progress. Default is TRUE.
...	additional arguments passed to NNLM::nnmf(...)

Value

Seurat object with NMF results in reduction slot. Program genes are stored in "misc" slot of NMF reduction slot.

Author(s)

Nicholas Mikolajewicz

References

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

See Also

nnmf

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