R/Constructors.R

In EuracBiomedicalResearch/FamAgg: Pedigree Analysis and Familial Aggregation

##********************************************************
##
##   FAData
##   that's the constructor for the FunAggrData class
##   * pedigree: the pedigree, can be a character string or a
##     data.frame
##   * age: the age, can
##   * header: for the internal read.table function that loads data.
##   * sep:
##
##********************************************************
FAData <- function(pedigree, age, trait, traitName, header = FALSE, sep = "\t",
                   id.col = "id", family.col = "family", father.col = "father",
                   mother.col = "mother", sex.col = "sex") {
    if(missing(pedigree)){
        stop("Argument pedigree has to be specified!")
    }
    if(missing(trait))
        trait <- logical()
    FSD <- new("FAData")
    expect_cn <- c(family = family.col, id = id.col, father = father.col,
                   mother = mother.col, sex = sex.col)
    ## processing pedigree
    if(is.character(pedigree)){
        ## means, we're loading the data.frame ourselfs.
        message(paste("Reading pedigree information from file ", pedigree,
                      "..."), appendLF=FALSE)
        pedigree <- doImport(pedigree, header = header, sep = sep,
                             id.col = id.col, family.col = family.col,
                             father.col = father.col, mother.col = mother.col,
                             sex.col = sex.col)
        ## Check if we've got eventually also the trait (i.e. from a ped or
        ## fam file).
        if(missing(trait) & any(colnames(pedigree) == "trait")){
            trait <- pedigree[, "trait"]
            pedigree <- pedigree[, colnames(pedigree) != "trait"]
        }
        pedigree <- pedigree[, names(expect_cn)]
        colnames(pedigree) <- expect_cn
        message("OK\n")
    }
    if (is.matrix(pedigree)) {
        ## transform to data.frame
        pedigree <- as.data.frame(pedigree, stringsAsFactors = FALSE)
    }
    if (!(is.data.frame(pedigree) | is(pedigree, "pedigree") |
          is(pedigree, "pedigreeList"))) {
        stop("Argument pedigree has to be a data.frame, a character string ",
             "specifying the file containing the pedigree, a pedigree object ",
             "or a pedigreeList object!")
    } else {
        if (is.data.frame(pedigree)) {
            CN <- .PEDCN
            if (!noColNames(pedigree)) {
                if (!all(expect_cn %in% colnames(pedigree)))
                    stop("Expected column names ",
                         paste0("'", expect_cn, "'", collapse = ", "),
                         " in 'pedigree' but I got ",
                         paste0("'", colnames(pedigree), "'", collapse = ", "))
                pedigree <- pedigree[, expect_cn]
                colnames(pedigree) <- names(expect_cn)
            } else {
                if (ncol(pedigree)!=length(CN))
                    stop("pedigree is expected to have ", length(CN),
                         " columns but I got ", ncol(pedigree), "!")
                warning("Forcing column names ", paste(CN, collapse=";"),
                        " on pedigree.")
                colnames(pedigree) <- CN
            }
        }
    }
    ## We don't like factors.
    if (is.factor(pedigree$id)) pedigree$id <- as.character(pedigree$id)
    ## Fixing the founders:
    if (is.factor(pedigree$father))
        pedigree$father <- as.character(pedigree$father)
    if (is.factor(pedigree$mother))
        pedigree$mother <- as.character(pedigree$mother)
    if (is.character(pedigree$father))
        pedigree$father[pedigree$father == ""] <- NA
    if (is.numeric(pedigree$father))
        pedigree$father[pedigree$father == 0] <- NA
    if (is.character(pedigree$mother))
        pedigree$mother[pedigree$mother == ""] <- NA
    if (is.numeric(pedigree$mother))
        pedigree$mother[pedigree$mother == 0] <- NA
    pedigree(FSD) <- pedigree
    ## processing age
    if(!missing(age)){
        if(is.character(age)){
            message(paste("Reading age information from file ", age, "..."),
                    appendLF=FALSE)
            FN <- age
            age <- read.table(age, header=header, sep=sep, as.is=TRUE)
            message("OK\n")
            ## assuming first column is the ID, second the age.
            warning("Assuming first column in ", FN,
                    " contains IDs and second age.")
            ageNames <- age[, 1]
            age <- age[ , 2]
            names(age) <- ageNames
        }
        if(!is.numeric(age)){
            stop("Argument age has to be a named numeric vector or a character",
                 " string specifying the file containing the age!")
        }
        age(FSD) <- age
    }
    if(!missing(traitName))
        FSD@traitname <- traitName
    ## Do we have a trait???
    if (length(trait)) {
        if (!all(is.na(trait))) {
            if (length(trait) == nrow(pedigree))
                if (is.null(names(trait)))
                    names(trait) <- as.character(pedigree$id)
            trait(FSD) <- trait
        }
    }
    if (validObject(FSD))
        FSD
}