R/accessory_funcs_2.R

In CompEpigen/methrix: Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

# Process all samples in one go (ideal for few number of samples)
merge_vect_code <- function(files, col_idx, col_data, ideal = FALSE, genome = NULL) {

    chr <- . <- NULL
    bdgs <- lapply(files, read_bdg, col_list = col_idx, genome = genome,
        fill_cpgs = FALSE)
    names(bdgs) <- rownames(col_data)
    if (ideal) {
        cov_mat <- data.frame(lapply(bdgs, function(x) x[, .(cov)]), stringsAsFactors = FALSE)
        beta_mat <- data.frame(lapply(bdgs, function(x) x[, .(beta)]),
            stringsAsFactors = FALSE)
        colnames(cov_mat) <- colnames(beta_mat) <- rownames(col_data)
        cov_mat <- cbind(bdgs[[1]][, .(chr, start)], cov_mat)
        beta_mat <- cbind(bdgs[[1]][, .(chr, start)], beta_mat)
    } else {
        bdgs <- data.table::rbindlist(l = bdgs, idcol = "sample")
        beta_mat <- data.table::dcast(bdgs, chr + start ~ sample, value.var = "beta")
        cov_mat <- data.table::dcast(bdgs, chr + start ~ sample, value.var = "cov",
            fill = 0)
    }
    rm(bdgs)
    gc()
    return(list(beta_matrix = beta_mat, cov_matrix = cov_mat))
}

#--------------------------------------------------------------------------------------------------------------------------

# Process samples in batches. Batches are processed in vectorized
# manner (ideal for large number of samples)
merge_vect_code_batch <- function(files, col_idx, batch_size, ideal = FALSE,
    col_data = NULL, genome = NULL) {

    chr <- . <- NULL
    batches <- split(files, ceiling(seq_along(files)/batch_size))
    batches_samp_names <- split(rownames(col_data), ceiling(seq_along(rownames(col_data))/batch_size))

    beta_mat_final <- data.table::data.table()
    cov_mat_final <- data.table::data.table()

    for (i in seq_along(batches)) {
        message(paste0("Processing batch ", i, " of ", length(batches)))
        batch_files <- batches[[i]]
        samp_names <- batches_samp_names[[i]]
        bdgs <- lapply(batch_files, read_bdg, col_list = col_idx, genome = genome,
            fill_cpgs = FALSE)
        names(bdgs) <- samp_names
        if (ideal) {
            if (i == 1) {
                cov_mat_final <- cbind(bdgs[[1]][, .(chr, start)], data.frame(lapply(bdgs,
                  function(x) x[, .(cov)]), stringsAsFactors = FALSE))
                beta_mat_final <- cbind(bdgs[[1]][, .(chr, start)], data.frame(lapply(bdgs,
                  function(x) x[, .(beta)]), stringsAsFactors = FALSE))
                colnames(cov_mat_final) <- colnames(beta_mat_final) <- c("chr",
                  "start", samp_names)
            } else {
                cov_mat <- data.frame(lapply(bdgs, function(x) x[, .(cov)]),
                  stringsAsFactors = FALSE)
                beta_mat <- data.frame(lapply(bdgs, function(x) x[, .(beta)]),
                  stringsAsFactors = FALSE)
                colnames(cov_mat) <- colnames(beta_mat) <- samp_names
                cov_mat_final <- cbind(cov_mat_final, cov_mat)
                beta_mat_final <- cbind(beta_mat_final, beta_mat)
            }
        } else {
            bdgs <- data.table::rbindlist(l = bdgs, idcol = "sample")
            if (i == 1) {
                beta_mat_final <- data.table::dcast(bdgs, chr + start ~
                  sample, value.var = "beta")
                cov_mat_final <- data.table::dcast(bdgs, chr + start ~
                  sample, value.var = "cov", fill = 0)
            } else {
                beta_mat_final <- merge(beta_mat_final, data.table::dcast(bdgs,
                  chr + start ~ sample, value.var = "beta"), by = c("chr",
                  "start"), all = TRUE)
                cov_mat_final <- merge(cov_mat_final, data.table::dcast(bdgs,
                  chr + start ~ sample, value.var = "cov", fill = 0), by = c("chr",
                  "start"), all = TRUE)
            }
        }
    }

    return(list(beta_matrix = data.table::setDT(beta_mat_final), cov_matrix = data.table::setDT(cov_mat_final)))
}

#--------------------------------------------------------------------------------------------------------------------------

# Use for loop for sample-by-sample processing.
merge_non_vect_code <- function(files, col_idx, coldata, verbose = TRUE,
    ideal = FALSE, genome = NULL) {

    chr <- . <- NULL
    beta_mat <- data.table::data.table()
    cov_mat <- data.table::data.table()

    for (i in seq_along(files)) {
        if (verbose) {
            message("Processing: ", files[i])
        }
        if (ideal) {
            if (i == 1) {
                b <- read_bdg(bdg = files[i], col_list = col_idx, genome = genome,
                  fill_cpgs = FALSE)
                beta_mat <- b[, .(chr, start, beta)]
                cov_mat <- b[, .(chr, start, cov)]
            } else {
                b <- read_bdg(bdg = files[i], col_list = col_idx, genome = genome,
                  fill_cpgs = FALSE)
                beta_mat <- cbind(beta_mat, b[, .(beta)])
                cov_mat <- cbind(cov_mat, b[, .(cov)])
            }
            colnames(beta_mat)[ncol(beta_mat)] <- colnames(cov_mat)[ncol(cov_mat)] <- rownames(coldata)[i]
        } else {
            if (i == 1) {
                b <- read_bdg(bdg = files[i], col_list = col_idx, genome = genome,
                  fill_cpgs = FALSE)
                beta_mat <- b[, .(chr, start, beta)]
                cov_mat <- b[, .(chr, start, cov)]
                colnames(beta_mat)[ncol(beta_mat)] <- colnames(cov_mat)[ncol(cov_mat)] <- rownames(coldata)[i]
            } else {
                b <- read_bdg(bdg = files[i], col_list = col_idx, genome = genome,
                  fill_cpgs = FALSE)
                beta_mat <- merge(beta_mat, b[, .(chr, start, beta)], by = c("chr",
                  "start"), all = TRUE)
                cov_mat <- merge(cov_mat, b[, .(chr, start, cov)], by = c("chr",
                  "start"), all = TRUE)
                colnames(beta_mat)[ncol(beta_mat)] <- colnames(cov_mat)[ncol(cov_mat)] <- rownames(coldata)[i]
            }
        }
    }
    mat_list <- list(beta_matrix = beta_mat, cov_matrix = cov_mat)
}