R/trfr.R

In RabadanLab/mutcomfocal: Analysis of copy number and mutation data.

trfr<-function(mcf, perms=NULL) UseMethod("trfr");
trfr.mcf_score<-function(mcf, perms=NULL) with(ref(mcf), {
    x2<-data.frame(gene[mcf[,1], 2:3], mcf[,2], 1:nrow(mcf), mcf[,1]);
    x2<-x2[order(x2[,1], x2[,2]),];

    res<-do10_2(x2[,3], x2[,1]);
    x2<-cbind(x2, res$x49_2);

    x5 <- unique(x2[,3]);
    x5 <- x5[order(-x5)];
    x5 <- cbind(x5, matrix(NA, length(x5), 3));
    x6<-tail(x2[,1],-1)==head(x2[,1],-1);
    for(i1 in 1:nrow(x5)) {
        x7 <- x2[,3]>=x5[i1, 1];
        x7_1 <- x7[-c(1, length(x7))];
        x7_h <- c(head(x7,1), x7_1);
        x7_t <- c(x7_1, tail(x7,1));
        if (!is.null(perms))
            x8 <- perms[,colnames(mcf)[2]]>=x5[i1, 1];
        x9 <- c(x7[1], x6&!x7_h&x7_t | !x6&x7_t)
        x5[i1, 2:4] <- c(sum(x7), sum(x9), ifelse(!is.null(perms), sum(x8), NA));
    }
    x5<-cbind(x5, x5[,2]/nrow(x2), x5[,4]/nrow(mcf));
    x5<-cbind(x5, ifelse(x5[,6]<=x5[,5], x5[,6]/x5[,5], 1));

    x10<-match(x2[,3], x5[,1]);
    x2<-cbind(x2, x5[x10, 2], x5[x10, 7], x5[x10, 3]);
    x2<-x2[order(x2[,4]), c(5, 3, 6:9)];
    colnames(x2)<-c(colnames(mcf), paste(colnames(mcf)[2], c("tier", "rank", "fdr", "regions"), sep="_"));
    class(x2)<-c("mcf_score", class(x2));
    ref(x2)<-ref(mcf);
    x2;
})