R/choose_markers.R

In cytolab/cytoMEM: Marker Enrichment Modeling (MEM)

choose_markers <- function(exp_data) {
    print("Numbered column names, in order they appear in file: ")
    print(paste(c(seq_len(
        ncol(exp_data) - 1
    )), ": ", colnames(exp_data[, c(seq_len(ncol(exp_data) - 1))]), sep = ""))
    markers1 <- readline("Enter column numbers to include (e.g. 1:5,6,8:10).\n")

    sep_vals <- unlist(strsplit(markers1, ","))
    list_vals <- vector()
    for (i in seq_len(length(sep_vals))) {
        val <- sep_vals[i]
        if (length(unlist(strsplit(val, ":"))) > 1) {
            new_val <- as.numeric(unlist(strsplit(val, ":"))[1]):as.numeric(unlist(strsplit(val, ":"))[2])
        } else{
            new_val <- as.numeric(sep_vals[i])
        }
        list_vals <- c(list_vals, new_val)
    }

    markerList <- c(list_vals, ncol(exp_data))

    return(markerList)
}