sclink_cor {scLink}

Calculate scLink's correlation matrix

Description

Calculate scLink's correlation matrix

Usage

sclink_cor(expr, ncores, nthre = 20, dthre = 0.9)

Arguments

expr

A gene expression matrix with rows representing cells and columns representing genes. Gene names are given as column names. Can be the output of sclink_norm or user constructed gene expression matrices.

ncores

Number of cores if using parallel computation.

nthre

An integer specifying a threshold on the number of complete observations. Defaults to 20.

dthre

A number specifying the threshold on dropout probabilities. Defaults to 0.9.

Value

A correlation matrix for gene co-expression relationships.

Author(s)

Wei Vivian Li, [e-mail]

Examples

count = readRDS(system.file("extdata", "example.rds", package = "scLink"))
count.norm = sclink_norm(count, scale.factor = 1e6, filter.genes = TRUE, n = 500)
corr = sclink_cor(expr = count.norm, ncores = 1)