runCorrelation: runCorrelation

In aertslab/SCENIC: SCENIC (Single Cell rEgulatory Network Inference and Clustering)

runCorrelation

Description

Calculates the spearman correlation on the input expression matrix & saves the results in SCENIC format

Usage

runCorrelation(exprMat_filtered, scenicOptions)

Arguments

exprMat_filtered	Expression matrix (filtered)
scenicOptions	Fields used: Intermediate file name "corrMat"

Value

Writes the output in the file name stored in: getIntName(scenicOptions, "corrMat")

Examples

library(SCENIC)
scenicOptions <- readRDS("int/scenicOptions.Rds")

loomPath <- system.file(package="SCENIC", "examples/mouseBrain_toy.loom")
exprMat <- SCopeLoomR::get_dgem(SCopeLoomR::open_loom(loomPath))

genesKept <- loadInt(scenicOptions, "genesKept")
exprMatrix_filtered <- exprMat[genesKept,]
exprMat_filtered <- log2(exprMatrix_filtered+1) 

runCorrelation(exprMat_filtered, scenicOptions)

aertslab/SCENIC documentation built on April 7, 2024, 10 a.m.