get_scores: Extract scone scores

In YosefLab/scone: Single Cell Overview of Normalized Expression data

Extract scone scores

Description

Extract scone scores

Usage

get_scores(x)

get_score_ranks(x)

## S4 method for signature 'SconeExperiment'
get_scores(x)

## S4 method for signature 'SconeExperiment'
get_score_ranks(x)

Arguments

x	an object of class SconeExperiment.

Value

get_scores returns a matrix with all (non-missing) scone scores, ordered by average score rank.

get_score_ranks returns a vector of average score ranks.

Examples

set.seed(42)
mat <- matrix(rpois(500, lambda = 5), ncol=10)
colnames(mat) <- paste("X", 1:ncol(mat), sep="")
obj <- SconeExperiment(mat)
res <- scone(obj, scaling=list(none=identity, uq=UQ_FN),
           evaluate=TRUE, k_ruv=0, k_qc=0,
           eval_kclust=2, bpparam = BiocParallel::SerialParam())
scores = get_scores(res)
score_ranks = get_score_ranks(res)

YosefLab/scone documentation built on Oct. 21, 2024, 4:39 p.m.