cAMARETTO_Results: cAMARETTO_Results To initiate the community AMARETTO this...

In broadinstitute/ImagingAMARETTO: ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

Description

cAMARETTO_Results

To initiate the community AMARETTO this results functions performs hyper geometric tests between all modules and gene sets.

Usage

cAMARETTO_Results(AMARETTOresults_all, NrCores = 1, output_dir = "./",
  gmt_filelist = NULL, drivers = FALSE)

Arguments

AMARETTOresults_all	A list of multiple AMARETTO_Run outputs. The names are run names.
NrCores	Nr of Cores that can be used to calculated the results.
output_dir	A directory that stores gmt files for the runs
gmt_filelist	A list with gmt files that are added into the communities. The names of the list are used in the networks. NULL if no list is added.
drivers	Boolean that defines if only targets or drivers and targets are used to calculate the HGT.

Value

a list with cAMARETTOresults data objects from multiple runs

Examples

Cibersortgmt <- "ciberSort.gmt"
cAMARETTOresults <- cAMARETTO_Results(AMARETTOresults_all, gmt_filelist=list(ImmuneSignature = Cibersortgmt), NrCores = 4 , output_dir = "./")

broadinstitute/ImagingAMARETTO documentation built on Dec. 3, 2019, 6:38 p.m.