importModulesGmt: importModules (deprecated)

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

importModules (deprecated)

Description

Imports TF co-expression from .gmt file, as generated by pySCENIC Deprecated: This function is no longer needed. The results can be loaded directly from the .loom file with get_regulons()

Usage

importModulesGmt(
  fileName,
  scenicOptions = NULL,
  saveAsDf = TRUE,
  verbose = TRUE
)

Arguments

fileName	File name of the co-expression modules (.gmt)
transpose	saveAsDf=TRUE to save as data.frame to continue the pipeline in R (with runSCENIC_2_createRegulons)

Value

Returns the co-expression modules as list (invisible), and saves them as data.frame if requested (file name: getIntName(scenicOptions, "tfModules_asDF"))

See Also

pySCENIC (https://pyscenic.readthedocs.io)

Examples

pyScenicDir <- "."
tfModules <- importModules(fileName=file.path(pyScenicDir,  "modules.gmt"))

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