R/annot_format.R

In mdgsa: Multi Dimensional Gene Set Analysis.

##format_annotation.r
##2010-07-16 dmontaner@cipf.es
##2013-03-25 dmontaner@cipf.es


##' @name annotMat2list
## @docType 
##' @author David Montaner \email{dmontaner@@cipf.es}
##' 
## @aliases 
##' 
##' @keywords annotation matrix list
##' @seealso \code{\link{annotList2mat}}, \code{\link{revList}}, \code{split}
##'
##' @title Convert an annotation matrix into an annotation list.
##' 
##' @description
##' Converts an annotation matrix to an annotation list.
##' The annotation matrix should have 2 columns, the first one with the
##' gene ids; the second one with the annotation ids.
##' 
##' @details
##' Each element of the annotation list represents a functional block;
##' it is a character vector containing the gene ids annotated under the
##' function.
##' The names of the list are the annotation ids.
##'
##' @param mat annotation matrix; gene IDs in the first column;
##' block IDs in the second column.
##' 
##' @return An annotation list: elements of the list are vectors of genes;
##' names of the list are Gene Set ids.
##' 
##' @examples
##' mat <- cbind (c("gen1", "gen2", "gen3"), c("Block1", "Block1", "Block2"))
##' annotMat2list (mat)
##' @export
annotMat2list <- function (mat) {
    
    mat <- as.matrix (mat) ## for data.frames
    dimnames (mat) <- NULL
    mat <- unique (mat)
    
    out <- split (x = mat[,1], f = mat[,2], drop = TRUE, sep = "")
  
    ## blocks <- unique (mat[,2])
    ## out <- list ()
    ## for (bk in blocks) {
    ##   out[[bk]] <- mat[mat[,2] == bk, 1]
    ## }
    
    out
}


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


##' @name annotList2mat
## @docType 
##' @author David Montaner \email{dmontaner@@cipf.es}
##' 
## @aliases 
##' 
##' @keywords annotation matrix list
##' @seealso \code{\link{annotMat2list}}, \code{\link{revList}}, \code{split}
##'
##' @title Convert an annotation list into an annotation matrix.
##'
##' @description
##' Converts an annotation list to an annotation matrix.
##' The annotation matrix should have 2 columns, the first one with the
##' gene ids;
##' the second one with the annotation ids.
##' 
##' @details
##' Each element of the annotation list represents a functional block;
##' it is a character vector containing the gene ids annotated under
##' the function.
##' The names of the list are the annotation ids.
##' 
##' @param lis annotation list.
##' @param tag substitutes missing list names if any.
##' 
##' @return An annotation matrix: the first column contains the gene or
##' feature ids,
##' the second column contains the Gene Set or functional block ids.
##' 
##' @examples
##' lis <- list (Block1 = c("gen1", "gen2"), Block2 = c("gen3"))
##' annotList2mat (lis)
##' 
##' @export
annotList2mat <- function (lis, tag = "listPos") {
  
    ## names (lis): may be NULL or contain NA
    ## tag: for missing list names tagging
    
    ## list   NAMES  go to column 2
    ## list ELEMENTS go to column 1 
    
    nombres <- names (lis)
    ##
    if (is.null (nombres)) {
        nombres <- paste (tag, 1:length (lis), sep = "")
    } else {
        esna <- is.na (nombres)
        nombres[esna] <- paste (tag, which (esna), sep = "")
    }    
    
    longitudes <- sapply (lis, length)
    
    v.nombres <- rep (nombres, times = longitudes)
    v.element <- unlist (lis)
    
    if (length (v.nombres) != length (v.element)) {
        tex <- "Matrix could not be reconstructed.
                Revise the structure of the input list."
        stop (gsub ("  +", "", tex))
    }
    
    salida <- cbind (v.element, v.nombres) ##consistent with annotMat2list
    ##
    dimnames (salida) <- NULL
    salida
}



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


##' @name revList
## @docType 
##' @author David Montaner \email{dmontaner@@cipf.es}
##' 
## @aliases 
##' 
##' @keywords revert annotation list
##' @seealso \code{\link{annotMat2list}}, \code{\link{revList}}
##' annotMat2list, annotList2mat
##'
##' @title Revert an annotation list.
##'
##' @description
##' Inverts a list: names to elements / elements to names
##' 
##' @param lis annotation list.
##' @param tag substitutes missing list names if any.
##' 
##' @return An inverted list. 
##' 
##' @examples
##' lis <- list (Block1 = c("gen1", "gen2"), Block2 = c("gen1", "gen3"))
##' revList (lis)
##' 
##' @export
revList <- function (lis, tag = "listPos") {
    
    annmat <- annotList2mat (lis)
    annmat <- annmat[,2:1]
    
    salida <- annotMat2list (annmat)
    salida
}