find.signature.genes: Find the signature genes for each group of cell/spots

In ProFAST: Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction

Find the signature genes for each group of cell/spots

Description

Find the signature genes for each group of cell/spots based on coembedding distance and expression ratio.

Usage

find.signature.genes(
  seu,
  distce.assay = "distce",
  ident = NULL,
  expr.prop.cutoff = 0.1,
  assay = NULL,
  genes.use = NULL
)

Arguments

seu	a Seurat object with coembedding in the reductions slot wiht component name reduction.
distce.assay	an optional character, specify the assay name that constains distance matrix beween cells/spots and features, default as 'distce' (distance of coembeddings).
ident	an optional character in columns of metadata, specify the group of cells/spots. Default as NULL, use Idents as the group.
expr.prop.cutoff	an optional postive real ranging from 0 to 1, specify cutoff of expression proportion of features, default as 0.1.
assay	an optional character, specify the assay in seu, default as NULL, representing the default assay in seu.
genes.use	an optional string vector, specify genes as the signature candidates.

Details

In each data.frame object of the returned value, the row.names are gene names, and these genes are sorted by decreasing order of 'distance'. User can define the signature genes as top n genes in distance and that the 'expr.prop' larger than a cutoff. We set the cutoff as 0.1.

Value

return a list with each component a data.frame object having two columns: 'distance' and 'expr.prop'.

References

None

See Also

None

Examples

library(Seurat)
data(pbmc3k_subset)
pbmc3k_subset <- pdistance(pbmc3k_subset, reduction='ncfm')
df_list_rna <- find.signature.genes(pbmc3k_subset)

ProFAST documentation built on April 3, 2025, 7:51 p.m.