Description Usage Arguments Value Examples
View source: R/cAMARETTO_Results.R
cAMARETTO_Results
To initiate the community AMARETTO this results functions performs hyper geometric tests between all modules and gene sets.
1 2 | cAMARETTO_Results(AMARETTOresults_all, NrCores = 1, output_dir = "./",
gmt_filelist = NULL, drivers = FALSE)
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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. |
a list with cAMARETTOresults data objects from multiple runs
1 2 | Cibersortgmt <- "ciberSort.gmt"
cAMARETTOresults <- cAMARETTO_Results(AMARETTOresults_all, gmt_filelist=list(ImmuneSignature = Cibersortgmt), NrCores = 4 , output_dir = "./")
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