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

Description Usage Arguments Value Examples

View source: R/cAMARETTO_Results.R

Description

cAMARETTO_Results

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

Usage

1
2
3
4
5
6
7
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

1
2
3
4
5
6
try(
cAMARETTOresults <- cAMARETTO_Results(AMARETTOresults_all,
  gmt_filelist=list(ImmuneSignature = Cibersortgmt),
  NrCores = 4 ,
  output_dir = "./")
)

broadinstitute/CommunityAMARETTO documentation built on April 6, 2020, 10:44 p.m.