R/genome_order.R

In genomicper: Circular Genomic Permutation using Genome Wide Association p-Values

genome_order <-
function (all_data = "") 
{
    rm_rs <- which(is.na(all_data[, 2]) == TRUE)
    print(paste("Number of SNPs without location and removed:", 
        length(rm_rs), sep = ""))
    if (length(rm_rs) != 0) {
        all_data <- all_data[-c(rm_rs), ]
    }
    rowsf <- length(unique(sort(as.character(all_data[, 4]))))
    colsf <- length(all_data)
    colnames(all_data)[4] <- "GENE_ID"
    for (i in 7:colsf) {
        all_data[, i] <- as.numeric(as.character(all_data[, i]))
    }
    or_data <- all_data
    or_data[, 2] <- as.character(or_data[, 2])
    
    
    lk <- c(1:50)
    lk <- as.character(lk)
    ## Numeric Chromosomes
 x <- which(or_data[,2] %in% lk)
 nums <- or_data[x,]
    nums[,2] <- as.numeric(nums[,2])
 indx_nums <- order(nums[,2],nums[,3])
 nums <- nums[indx_nums,]
    
    ## Chromosome LETTERS 
    lets <- or_data[-c(x),]
 indx_lets <- order(lets[,2],lets[,3])
 lets <- lets[indx_lets,]

 # bind both datasets
    or_data <- rbind(nums,lets)
# unique genes
    listf <- unique(sort(or_data[, 4]))
    gs_locs <- matrix(data = NA, nrow = rowsf, ncol = 6)
    for (j in 1:length(listf)) {
        ids <- which(or_data[, 4] == listf[j])
        obs <- length(ids)
        gs_locs[j, 1] <- as.character(or_data[ids[1], 5])
        gs_locs[j, 2] <- or_data[ids[1], 2]
        gs_locs[j, 3] <- or_data[ids[1], 3]
        gs_locs[j, 4] <- listf[j]
        gs_locs[j, 5] <- ids[1]
        gs_locs[j, 6] <- obs
    }
    lab <- c("Symbol", "Chromosome", "Location", "Gene_ID", "Start_Indx", 
        "Observations")
    colnames(gs_locs) <- lab
    ordered_alldata <- or_data
    return(list(ordered_alldata = ordered_alldata, gs_locs = gs_locs))
}