sclink_cor {scLink} | R Documentation |
Calculate scLink's correlation matrix
sclink_cor(expr, ncores, nthre = 20, dthre = 0.9)
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 |
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. |
A correlation matrix for gene co-expression relationships.
Wei Vivian Li, vivian.li@rutgers.edu
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)