sclink_cor: Calculate scLink's correlation matrix
In scLink: Inferring Functional Gene Co-Expression Networks from Single Cell Data

Description Usage Arguments Value Author(s) Examples

View source: R/main.R

Calculate scLink's correlation matrix

1	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 `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.

A correlation matrix for gene co-expression relationships.

Wei Vivian Li, vivian.li@rutgers.edu

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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)