robustSingleCell (version 0.1.1)

controlled.mean.score: Compute Controlled Activation Score

Description

Compute mean gene signatures activation scores while controlling for technically similar genes.

Usage

controlled.mean.score(environment, genes, knn = 10,
  exclude.missing.genes = T, constrain.cell.universe = NA)

Arguments

environment

environment object

genes

gene list upon which to calculate gene signature activate

knn

number of nearest neighbors

exclude.missing.genes

whether to exclude genes with missing values

constrain.cell.universe

binary vector indicating in which subset of cells to calculate the gene signature activation. Default is all cells.

Value

gene signature activation scores per cell

Examples

# NOT RUN {
LCMV1 <- setup_LCMV_example()
exhaustion_markers <- c('Pdcd1', 'Cd244', 'Havcr2', 'Ctla4', 'Cd160', 'Lag3',
'Tigit', 'Cd96')
Exhaustion <- controlled.mean.score(LCMV1, exhaustion_markers)
# }