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Original file line number | Diff line number | Diff line change |
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@@ -1,39 +1,39 @@ | ||
#' @export pathSim | ||
setGeneric("pathSim", function(pathway1, pathway2, info, ...) | ||
standardGeneric("pathSim") | ||
) | ||
|
||
#' @export mpathSim | ||
setGeneric("mpathSim", function(pathways, info, method, ...) | ||
standardGeneric("mpathSim") | ||
) | ||
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||
#' @export geneSim | ||
setGeneric("geneSim", function(gene1, gene2, info, method, ...) | ||
standardGeneric("geneSim") | ||
) | ||
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#' @export mgeneSim | ||
setGeneric("mgeneSim", function(genes, info, method, ....) | ||
standardGeneric("mgeneSim") | ||
) | ||
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#' @export clusterSim | ||
setGeneric("clusterSim", function(cluster1, cluster2, info, method, ...) | ||
standardGeneric("clusterSim") | ||
) | ||
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#' @export mclusterSim | ||
setGeneric("mclusterSim", function(clusters, info, method, ....) | ||
standardGeneric("mclusterSim") | ||
) | ||
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#' @export clusterGeneSim | ||
setGeneric("clusterGeneSim", function(cluster1, cluster2, info, method, ...) | ||
standardGeneric("clusterGeneSim") | ||
) | ||
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#' @export mclusterGeneSim | ||
setGeneric("mclusterGeneSim", function(clusters, info, method, ....) | ||
standardGeneric("mclusterGeneSim") | ||
) | ||
#' @export pathSim | ||
setGeneric("pathSim", function(pathway1, pathway2, info, ...) | ||
standardGeneric("pathSim") | ||
) | ||
|
||
#' @export mpathSim | ||
setGeneric("mpathSim", function(pathways, info, method, ...) | ||
standardGeneric("mpathSim") | ||
) | ||
|
||
#' @export geneSim | ||
setGeneric("geneSim", function(gene1, gene2, info, method, ...) | ||
standardGeneric("geneSim") | ||
) | ||
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||
#' @export mgeneSim | ||
setGeneric("mgeneSim", function(genes, info, method, ....) | ||
standardGeneric("mgeneSim") | ||
) | ||
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||
#' @export clusterSim | ||
setGeneric("clusterSim", function(cluster1, cluster2, info, method, ...) | ||
standardGeneric("clusterSim") | ||
) | ||
|
||
#' @export mclusterSim | ||
setGeneric("mclusterSim", function(clusters, info, method, ....) | ||
standardGeneric("mclusterSim") | ||
) | ||
|
||
#' @export clusterGeneSim | ||
setGeneric("clusterGeneSim", function(cluster1, cluster2, info, method, ...) | ||
standardGeneric("clusterGeneSim") | ||
) | ||
|
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#' @export mclusterGeneSim | ||
setGeneric("mclusterGeneSim", function(clusters, info, method, ....) | ||
standardGeneric("mclusterGeneSim") | ||
) |
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Original file line number | Diff line number | Diff line change |
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@@ -1,25 +1,19 @@ | ||
#' BioCor: A package to calculate functional similarities | ||
#' | ||
#' Calculates a functional similarity measure between gene identifiers | ||
#' based on the pathways described on KEGG and REACTOME. | ||
#' | ||
#' @section Important functions: | ||
#' \describe{ | ||
#' \item{[pathSim()]}{Calculates the similarity between two pathways} | ||
#' \item{[geneSim()]}{Calculates the similarity (based on pathSim) | ||
#' between two genes} | ||
#' \item{[clusterSim()]}{Calculates the similarity between two | ||
#' clusters of genes by joining pathways of each gene.} | ||
#' \item{[clusterGeneSim()]}{Calculates the similarity between two | ||
#' clusters of genes by comparing the similarity between the genes of a cluster | ||
#' } | ||
#' \item{[similarities()]}{Allows to combine the value of matrices of | ||
#' similarities} | ||
#' \item{[conversions()]}{Two functions to convert similarity | ||
#' measures} | ||
#' \item{[weighted()]}{Functions provided to combine similarities} | ||
#' } | ||
#' @name BioCor-package | ||
#' @aliases BioCor | ||
#' @docType package | ||
NULL | ||
#' BioCor: A package to calculate functional similarities | ||
#' | ||
#' Calculates a functional similarity measure between gene identifiers | ||
#' based on the pathways described on KEGG and REACTOME. | ||
#' | ||
#' @section Important functions: | ||
#' - **[pathSim()]**: Calculates the similarity between two pathways. | ||
#' - **[geneSim()]**: Calculates the similarity (based on pathSim) | ||
#' between two genes. | ||
#' - **[clusterSim()]**: Calculates the similarity between two | ||
#' clusters of genes by joining pathways of each gene. | ||
#' - **[clusterGeneSim()]**: Calculates the similarity between two | ||
#' clusters of genes by comparing the similarity between the genes of a cluster. | ||
#' - **[similarities()]**: Allows to combine the value of matrices of | ||
#' similarities. | ||
#' - **[conversions()]**: Two functions to convert similarity | ||
#' measures. | ||
#' - **[weighted()]**: Functions provided to combine similarities. | ||
'_PACKAGE' |
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