R/matchFeatures.R

In iC10: A Copy Number and Expression-Based Classifier for Breast Tumours

matchFeatures <-
function (CN = NULL, Exp = NULL, CN.by.feat = c("gene", "probe"),
    Exp.by.feat = c("gene", "probe"), ref = "hg19")
{
    if (length(CN.by.feat) == 2) {
        CN.by.feat <- "probe"
    }
    if (length(Exp.by.feat) == 2) {
        Exp.by.feat <- "gene"
    }
    IntClustMemb <- NULL
    data(Map.CN, envir = environment())
    data(Map.Exp, envir = environment())
    data(train.CN, envir = environment())
    data(train.Exp, envir = environment())
    data(IntClustMemb, envir = environment())
    data(Map.All, envir = environment())
    if (!is.null(CN) & is.null(Exp)) {
        if (CN.by.feat == "probe") {
            Probes <- Map.All$Probe_ID
            Synonyms <- NULL
            train.CN <- as.matrix(train.CN)
        }
        else {
            Map.All <- Map.All[which(Map.All$Gene.Chosen == "YES"),
                ]
            Probes <- as.character(Map.All$Gene_symbol)
            Synonyms <- as.character(Map.All$Synonyms_0)
            tmp <- rep(Probes, sapply(strsplit(Synonyms, ";"),
                length))
            Synonyms <- do.call("c", strsplit(Synonyms, ";"))
            Synonyms <- gsub(" ", "", Synonyms)
            names(Synonyms) <- tmp
            Synonyms <- Synonyms[which(!is.na(Synonyms))]
            train.CN <- as.matrix(train.CN[Map.All$Probe_ID,
                ])
            rownames(train.CN) <- Map.All$Gene_symbol
        }
        CN <- getCNfeatures(CN, Probes, Map.All, CN.by.feat,
            ref, Synonyms)
        all.na <- which(apply(CN, 1, function(x) mean(is.na(x))) <
            1)
        CN <- CN[all.na, ]
        train.CN <- train.CN[all.na, ]
        Map.CN <- Map.All[all.na, ]
        Map.Exp <- NULL
        train.Exp <- NULL
    }
    if (!is.null(CN) & !is.null(Exp)) {
        if (Exp.by.feat == "probe") {
            Probes <- Map.Exp$Probe_ID
            Synonyms <- as.character(Map.Exp$Synonyms_0)
            tmp <- rep(Probes, sapply(strsplit(Synonyms, ";"),
                length))
            Synonyms <- do.call("c", strsplit(Synonyms, ";"))
            Synonyms <- gsub(" ", "", Synonyms)
            names(Synonyms) <- tmp
            Synonyms <- Synonyms[which(!is.na(Synonyms))]
            train.Exp <- train.Exp[Map.Exp$Probe_ID, ]
        }
        else {
            Map.Exp <- Map.Exp[which(Map.Exp$Gene.Chosen == "YES"),
                ]
            Probes <- as.character(Map.Exp$Gene_symbol)
            Synonyms <- as.character(Map.Exp$Synonyms_0)
            tmp <- rep(Probes, sapply(strsplit(Synonyms, ";"),
                length))
            Synonyms <- do.call("c", strsplit(Synonyms, ";"))
            Synonyms <- gsub(" ", "", Synonyms)
            names(Synonyms) <- tmp
            Synonyms <- Synonyms[which(!is.na(Synonyms))]
            train.Exp <- train.Exp[Map.Exp$Probe_ID, ]
            rownames(train.Exp) <- Map.Exp$Gene_symbol
        }
        if (CN.by.feat == "probe") {
            Probes.CN <- Map.CN$Probe_ID
            Synonyms.CN <- NULL
            train.CN <- as.matrix(train.CN[Map.CN$Probe_ID, ])
        }
        else {
            tmp.map <- Map.All[, c("Probe_ID", "Synonyms_0")]
            Map.CN <- merge(Map.CN, tmp.map, sort = FALSE)
            rownames(Map.CN) <- Map.CN$Probe_ID
            Probes.CN <- as.character(Map.CN$Gene_symbol)
            Synonyms.CN <- as.character(Map.CN$Synonyms_0)
            tmp <- rep(Probes.CN, sapply(strsplit(Synonyms.CN,
                ";"), length))
            Synonyms.CN <- do.call("c", strsplit(Synonyms.CN,
                ";"))
            Synonyms.CN <- gsub(" ", "", Synonyms.CN)
            names(Synonyms.CN) <- tmp
            Synonyms.CN <- Synonyms.CN[which(!is.na(Synonyms.CN))]
            train.CN <- as.matrix(train.CN[rownames(Map.CN),
                ])
            rownames(train.CN) <- Map.CN$Gene_symbol
        }
        CN <- getCNfeatures(CN, Probes.CN, Map.CN, CN.by.feat,
            ref, Synonyms.CN)
        Exp <- getExpfeatures(Exp, Probes, Synonyms, Exp.by.feat)
        common.cols <- intersect(colnames(Exp), colnames(CN))
        Exp <- Exp[, which(colnames(Exp) %in% common.cols)]
        CN <- CN[, which(colnames(CN) %in% common.cols)]
        CN <- CN[, match(colnames(Exp), colnames(CN))]
        all.na <- which(apply(Exp, 1, function(x) mean(is.na(x))) <
            1)
        Exp <- Exp[all.na, ]
        train.Exp <- train.Exp[all.na, ]
        Map.Exp <- Map.Exp[all.na, ]
        all.na <- which(apply(CN, 1, function(x) mean(is.na(x))) <
            1)
        CN <- CN[all.na, ]
        train.CN <- train.CN[all.na, ]
        Map.CN <- Map.CN[all.na, ]
        train.Exp <- as.matrix(train.Exp)
    }
    if (!is.null(Exp) & is.null(CN)) {
        if (Exp.by.feat == "probe") {
            Probes <- Map.All$Probe_ID
            Synonyms <- as.character(Map.All$Synonyms_0)
            tmp <- rep(Probes, sapply(strsplit(Synonyms, ";"),
                length))
            Synonyms <- do.call("c", strsplit(Synonyms, ";"))
            Synonyms <- gsub(" ", "", Synonyms)
            names(Synonyms) <- tmp
            Synonyms <- Synonyms[which(!is.na(Synonyms))]
        }
        else {
            Map.All <- Map.All[which(Map.All$Gene.Chosen == "YES"),
                ]
            Probes <- as.character(Map.All$Gene_symbol)
            Synonyms <- as.character(Map.All$Synonyms_0)
            tmp <- rep(Probes, sapply(strsplit(Synonyms, ";"),
                length))
            Synonyms <- do.call("c", strsplit(Synonyms, ";"))
            Synonyms <- gsub(" ", "", Synonyms)
            names(Synonyms) <- tmp
            Synonyms <- Synonyms[which(!is.na(Synonyms))]
            train.Exp <- train.Exp[Map.All$Probe_ID, ]
            rownames(train.Exp) <- Map.All$Gene_symbol
        }
        Exp <- getExpfeatures(Exp, Probes, Synonyms, Exp.by.feat)
        all.na <- which(apply(Exp, 1, function(x) mean(is.na(x))) <
            1)
        Exp <- Exp[all.na, ]
        train.Exp <- train.Exp[all.na, ]
        train.CN <- NULL
        train.Exp <- as.matrix(train.Exp)
        Map.CN <- NULL
        Map.Exp <- Map.All[all.na, ]
    }
    res <- list(CN = CN, Exp = Exp, train.CN = train.CN, train.Exp = train.Exp,
        train.iC10 = IntClustMemb, map.cn = Map.CN, map.exp = Map.Exp)
    attr(res, "CN.by.feat") <- CN.by.feat
    attr(res, "Exp.by.feat") <- Exp.by.feat
    attr(res, "ref") <- ref
    res
}