GenerateCellSignature: Generate single-cell gene signature for ligand activity...

In BlishLab/scriabin: Single-cell resolved interaction analysis through binning

Generate single-cell gene signature for ligand activity ranking

Description

Generate single-cell gene signature for ligand activity ranking

Usage

GenerateCellSignature(seu, variant_genes, dq = 0.05)

Arguments

seu	A seurat object
variant_genes	character vector of genes to use for gene-signature calculation. This list of genes should comprise genes that are variable across the biological axis of interest. Eg. for single datasets, this may simply be the dataset's HVGs. For a longitudinal dataset, these may be genes that change over time. Use IDVariantGenes to identify genes that vary across time, between groups, etc.
dq	numeric. Distance quantile. Genes that are further away than this quantile threshold will not be considered part of a cell's gene signature and not used for ligand activity prediction

Value

Returns a matrix where columns are cells, rows are genes, and values are binary corresponding to if that gene appears in that cell's gene signature

References

Cortal, et al. Nat Biotech (2021)

BlishLab/scriabin documentation built on Sept. 16, 2024, 1:19 a.m.