R/get_rank_tables_from_rra.R

In scMAGeCK: Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening data

get_rank_tables_from_rra <- function(rankexp, bc_dox_u, rrapath = NULL, pcutoff = 0.3, tmpprefix = paste("sample_", 
    runif(1, 1, 10000), sep = ""), negctrlgenelist = "NonTargetingControlGuideForHuman", more_rra = "", 
    negsel = TRUE, possel = TRUE, keeptmp = FALSE) {
    rankexp = rankexp[names(rankexp) %in% rownames(bc_dox_u) & !is.na(bc_dox_u[names(rankexp), "barcode"])]
    if (length(rankexp) < 3) {
        message("Error: cannot find enough cells.")
        return(NULL)
    }
    rankexp = sort(rankexp)
    
    texp_guide_ass = bc_dox_u[names(rankexp), "barcode"]
    texp_gene_ass = bc_dox_u[names(rankexp), "gene"]
    texp_guide_ass1 = paste(texp_guide_ass, 1:length(texp_guide_ass), sep = "_r")
    
    rra_oframe = data.frame(guide = texp_guide_ass1, gene = texp_gene_ass, list = rep("list", length(texp_guide_ass)), 
        value = rankexp, prob = rep(1, length(texp_guide_ass)), chosen = rep(1, length(texp_guide_ass)))
    low_file = paste(tmpprefix, "_rra_low.txt", sep = "")
    write.table(rra_oframe, file = low_file, row.names = FALSE, quote = FALSE, sep = "\t")
    
    
    rra_oframe_h = rra_oframe
    rra_oframe_h[, "value"] = -1 * rra_oframe_h[, "value"]
    rra_oframe_h = rra_oframe_h[order(rra_oframe_h[, "value"]), ]
    high_file = paste(tmpprefix, "_rra_high.txt", sep = "")
    write.table(rra_oframe_h, file = high_file, row.names = FALSE, quote = FALSE, sep = "\t")
    ngguidefile = paste(tmpprefix, "_negctrl.txt", sep = "")
    
    if (!is.null(negctrlgenelist)) {
        ngguidelist = texp_guide_ass1[texp_gene_ass %in% negctrlgenelist]
        write.table(ngguidelist, file = ngguidefile, sep = "\t", row.names = FALSE, col.names = FALSE, 
            quote = FALSE)
        ngguidecommand = paste("--control", ngguidefile)
    } else {
        ngguidecommand = ""
    }
    if (is.null(rrapath)) {
        rracommand = "RRA"
    } else {
        rracommand = rrapath
    }
    
    rra_low_out = paste(tmpprefix, "_rra_low.out", sep = "")
    rra_c = paste(rracommand, "-i", low_file, "-o", rra_low_out, ngguidecommand, "-p", pcutoff, "--max-sgrnapergene-permutation 10000 ", 
        more_rra)
    if (negsel) {
        message(rra_c)
        system(rra_c, ignore.stdout = TRUE, ignore.stderr = TRUE)
    }
    
    rra_high_out = paste(tmpprefix, "_rra_high.out", sep = "")
    rra_c = paste(rracommand, "-i", high_file, "-o", rra_high_out, ngguidecommand, "-p", pcutoff, "--max-sgrnapergene-permutation 10000 ", 
        more_rra)
    if (possel) {
        message(rra_c)
        system(rra_c, ignore.stdout = TRUE, ignore.stderr = TRUE)
    }
    
    # merge both
    if (negsel) {
        frame_l = read.table(rra_low_out, header = TRUE, as.is = TRUE, row.names = 1, na.strings = "")
    }
    if (possel) {
        frame_h = read.table(rra_high_out, header = TRUE, as.is = TRUE, row.names = 1, na.strings = "")
    }
    
    if (negsel & !possel) {
        system(paste("rm", low_file, rra_low_out))
        if (!is.null(negctrlgenelist)) {
            system(paste("rm", ngguidefile))
        }
        return(frame_l)
    }
    if (!negsel & possel) {
        system(paste("rm", high_file, rra_high_out))
        if (!is.null(negctrlgenelist)) {
            system(paste("rm", ngguidefile))
        }
        return(frame_h)
    }
    report_f = merge(frame_l, frame_h, by = 0, suffixes = c(".low", ".high"))
    
    if (!keeptmp) {
        system(paste("rm", low_file, high_file, rra_low_out, rra_high_out))
        if (!is.null(negctrlgenelist)) {
            system(paste("rm", ngguidefile))
        }
    }
    return(report_f)
}
TRUE