mdgsa: Multi Dimensional Gene Set Analysis.

##propagateGO.r
##2013-04-03 dmontaner@cipf.es
##2014-10-10 dmontaner@cipf.es

## To Do
## Eliminate almost all warnings.

##' @name propagateGO
## @docType 
##' @author David Montaner \email{dmontaner@@cipf.es}
##' 
## @aliases 
##' 
##' @keywords propagate GO gene ontology
##' @seealso \code{\link{annotMat2list}}, \code{\link{annotFilter}}
##'
##' @title Propagate Gene Ontology annotation.
##' 
##' @description
##' Genes annotated under a GO term inherit the annotation from
##' all its ancestors.
##' 
##' @details
##' Uses the library GO.db.
##' 
##' @param annot annotation list or matrix.
##' @param verbose verbose
##'
##' @return A annotation matrix or list with the propagated annotation.
##'
##' @examples
##' mat <- cbind (c("gene1", "gene2"), c("GO:0034390", "GO:0042889"))
##' mat
##' propagateGO (mat)
##'
##' li <- list ('GO:0034390' = "gene1", 'GO:0042889' = "gene2")
##' li
##' propagateGO (li)
##'
##' @importFrom AnnotationDbi as.list
##' @import GO.db
##' 
##' @export
propagateGO <- function (annot, verbose = FALSE) {
  
    if (is.matrix (annot) | is.data.frame (annot)) {
        annot <- propagateGO.matrix (annot, verbose = verbose)
    }
    
    if (is.list (annot)) {
        annot <- annotList2mat (annot)
        annot <- propagateGO.matrix (annot, verbose = verbose)
        annot <- annotMat2list (annot)
    }
    
    annot
}


################################################################################


## @name propagateGO.matrix
## 
## @author David Montaner \email{dmontaner@@cipf.es}
##
## @keywords propagate GO gene ontology matrix
## 
## @seealso \code{\link{propagateGO}}
##
## @title Propagate Gene Ontology annotations for annotation matrices.
## 
## @description
## Genes annotated under a GO term inherit the annotation from
## all its ancestors.
## 
## @details
## Uses the library GO.db.
##
## @param annotation annotation list or matrix
## @param verbose verbose.
## 
## @return A annotation matrix with the propagated annotation.
##
## @importFrom AnnotationDbi as.list
## @import GO.db
## @export
propagateGO.matrix <- function (annotation, verbose = TRUE) {

    if (verbose) {
        message ("Using GO.db version: ",
                 packageDescription ("GO.db", fields = "Version"))
    }
    
    columnas <- colnames (annotation)
    annotation <- as.matrix (annotation)
    dimnames (annotation) <- NULL

    ##Removing duplicated annotations 1
    ##duplicados <- duplicated (annotation)
    ## Much faster:
    duplicados <- duplicated (paste (annotation[,1], annotation[,2]))
    annotation <- annotation[!duplicados,]
    
    ##Getting ancestor GO terms
    ancestros <- c (as.list (GOBPANCESTOR),
                    as.list (GOMFANCESTOR),
                    as.list (GOCCANCESTOR))
    
    ##Propagating
    ancestros.ordenados <- ancestros[annotation[,2]]
    longitudes <- sapply (ancestros.ordenados, length,  USE.NAMES = FALSE)
    heredados <- cbind (rep (annotation[,1], times = longitudes),
                        unlist (ancestros.ordenados))
    rownames (heredados) <- NULL
    
    ## Matrix format
    annotation <- rbind (annotation, heredados)
    
    ## Remove "all" term
    noees.all <- annotation[,2] != "all"
    annotation <- annotation[noees.all,]

    ##Removing duplicated annotations 1
    ##duplicados <- duplicated (annotation)
    ## Much faster:
    duplicados <- duplicated (paste (annotation[,1], annotation[,2]))
    annotation <- annotation[!duplicados,]

    ## ids
    colnames (annotation) <- columnas

    ## OUTPUT
    annotation
}