run.rwr: 4.1 To calculate the label propagation probability for a gene...

In gsdensity: Density-Based Gene Set Specificity Evaluation

4.1 To calculate the label propagation probability for a gene set among cells; result in a vector (length = number of cells) reflecting the probability each cell is labeled during the propagation (relevance to the gene set)

Description

4.1 To calculate the label propagation probability for a gene set among cells; result in a vector (length = number of cells) reflecting the probability each cell is labeled during the propagation (relevance to the gene set)

Usage

run.rwr(el, gene_set, cells, restart = 0.75)

Arguments

el	edge list; output of 'compute.nn.edges'
gene_set	a vector of genes of interest
cells	name of cells; usually the same as 'colnames(object)'
restart	the probability of the propagation to restart

Value

cell vector (representing gene set activity)

Examples

cells <- colnames(pbmc.mtx)
el <- gsdensity::compute.nn.edges(coembed = ce, nn.use = 300)
cv <- run.rwr(el = el, gene_set = gene.set.list[1], cells = cells)

gsdensity documentation built on March 31, 2023, 8:32 p.m.