MomaConstructor {MOMA} | R Documentation |
Create MOMA Object from either a MultiAssayExperiment object or a list of assays. See vignette for more information on how to set up and run the MOMA object
MomaConstructor( x, pathways, gene.blacklist = NA_character_, output.folder = NA_character_, gene.loc.mapping = gene.map, viperAssay = "viper", mutMat = "mut", cnvMat = "cnv", fusionMat = "fusion" )
x |
A MultiAssayExerperiment object or list object with the following assays: (note: by default assays must have these exact names. Otherwise they can be changed using the viperAssay, mutMat, cnvMat and fusionMat parameters.)
|
pathways |
A named list of lists. Each named list represents interactions between proteins (keys) and their associated partners |
gene.blacklist |
A vector of genes to exclude from the analysis |
output.folder |
Location to store output and intermediate results |
gene.loc.mapping |
A data.frame of band locations and Entrez IDs |
viperAssay |
name associated with the viper assay in the assay object |
mutMat |
name associated with the mutation matrix in the assay object |
cnvMat |
name associated with the cnv matrix in the assay object |
fusionMat |
name associated with the fusion matrix in the assay object |
an instance of class Moma
momaObj <- MomaConstructor(example.gbm.mae, gbm.pathways)