R/data.R

In ProgModule: Identification of Prognosis-Related Mutually Exclusive Modules

#' @title maf_data, MAF file
#' @description maf_data, The patients' somatic mutation data, which in MAF format.
#' @usage maf_data
"maf_data"

#' @title module, gene set
#' @description module, Original modular gene set.
#' @usage module
"module"

#' @title net, network
#' @description net, Is a local network extracted from the ppi network.
#' @usage net
"net"

#' @title mut_status, mutations matrix
#' @description mut_status, the mutations matrix,generated by `get_mut_status`.
#' @usage mut_status
"mut_status"

#' @title subnet, network
#' @description subnet, Is a maximum connected subnet,extracted by mapping all genes to the ppi network.
#' @usage subnet
"subnet"

#' @title local_network, local network gene set
#' @description local_network, the local network gene set of each gene by breadth-first algorithm,,generated by `get_local_network`.
#' @usage local_network
"local_network"



#' @title candidate_module, candidate module
#' @description candidate_module, Is the gene set from each local network by greedy algorithm,generated by `get_candidate_module`.
#' @usage candidate_module
"candidate_module"

#' @title final_candidate_module, Final candidate modules
#' @description final_candidate_module, Is the final candidate module by intersecting modules from three protein networks in pairs,generated by `get_final_candidate_module`.
#' @usage final_candidate_module
"final_candidate_module"

#' @title plotMutInteract_moduledata
#' @description The data use for drawing mutually exclusive and co-occurrence plots.
#' @usage plotMutInteract_moduledata
"plotMutInteract_moduledata"

#' @title plotMutInteract_mutdata
#' @description The data use for drawing mutually exclusive and co-occurrence plots.
#' @usage plotMutInteract_mutdata
"plotMutInteract_mutdata"

#' @title univarCox_result
#' @description The result of Cox univariate analysis,generated by `get_univarCox_result`.
#' @usage univarCox_result
"univarCox_result"