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00-AllClasses.R
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##' Class "compareClusterResult"
##' This class represents the comparison result of gene clusters by GO
##' categories at specific level or GO enrichment analysis.
##'
##'
##' @name compareClusterResult-class
##' @aliases compareClusterResult-class show,compareClusterResult-method
##' summary,compareClusterResult-method plot,compareClusterResult-method
##' @docType class
##' @slot compareClusterResult cluster comparing result
##' @slot geneClusters a list of genes
##' @slot fun one of groupGO, enrichGO and enrichKEGG
##' @slot gene2Symbol gene ID to Symbol
##' @slot keytype Gene ID type
##' @slot readable logical flag of gene ID in symbol or not.
##' @slot .call function call
##' @slot termsim Similarity between term
##' @slot method method of calculating the similarity between nodes
##' @slot dr dimension reduction result
##' @exportClass compareClusterResult
##' @author Guangchuang Yu \url{https://yulab-smu.top}
##' @exportClass compareClusterResult
##' @seealso
##' \code{\linkS4class{enrichResult}}
##' @keywords classes
setClass("compareClusterResult",
representation = representation(
compareClusterResult = "data.frame",
geneClusters = "list",
fun = "character",
gene2Symbol = "character",
keytype = "character",
readable = "logical",
.call = "call",
termsim = "matrix",
method = "character",
dr = "list"
)
)
##' Class "enrichResult"
##' This class represents the result of enrichment analysis.
##'
##'
##' @name enrichResult-class
##' @aliases enrichResult-class
##' show,enrichResult-method summary,enrichResult-method
##'
##' @docType class
##' @slot result enrichment analysis
##' @slot pvalueCutoff pvalueCutoff
##' @slot pAdjustMethod pvalue adjust method
##' @slot qvalueCutoff qvalueCutoff
##' @slot organism only "human" supported
##' @slot ontology biological ontology
##' @slot gene Gene IDs
##' @slot keytype Gene ID type
##' @slot universe background gene
##' @slot gene2Symbol mapping gene to Symbol
##' @slot geneSets gene sets
##' @slot readable logical flag of gene ID in symbol or not.
##' @slot termsim Similarity between term
##' @slot method method of calculating the similarity between nodes
##' @slot dr dimension reduction result
##' @exportClass enrichResult
##' @author Guangchuang Yu \url{https://yulab-smu.top}
##' @seealso \code{\link{enrichDO}}
##' @keywords classes
setClass("enrichResult",
representation=representation(
result = "data.frame",
pvalueCutoff = "numeric",
pAdjustMethod = "character",
qvalueCutoff = "numeric",
organism = "character",
ontology = "character",
gene = "character",
keytype = "character",
universe = "character",
gene2Symbol = "character",
geneSets = "list",
readable = "logical",
termsim = "matrix",
method = "character",
dr = "list"
),
prototype=prototype(readable = FALSE)
)
##' Class "gseaResult"
##' This class represents the result of GSEA analysis
##'
##'
##' @name gseaResult-class
##' @aliases gseahResult-class
##' show,gseaResult-method summary,gseaResult-method
##'
##' @docType class
##' @slot result GSEA anaysis
##' @slot organism organism
##' @slot setType setType
##' @slot geneSets geneSets
##' @slot geneList order rank geneList
##' @slot keytype ID type of gene
##' @slot permScores permutation scores
##' @slot params parameters
##' @slot gene2Symbol gene ID to Symbol
##' @slot readable whether convert gene ID to symbol
##' @slot dr dimension reduction result
##' @exportClass gseaResult
##' @author Guangchuang Yu \url{https://yulab-smu.top}
##' @keywords classes
setClass("gseaResult",
representation = representation(
result = "data.frame",
organism = "character",
setType = "character",
geneSets = "list",
geneList = "numeric",
keytype = "character",
permScores = "matrix",
params = "list",
gene2Symbol = "character",
readable = "logical",
termsim = "matrix",
method = "character",
dr = "list"
)
)