data-raw/pbmc_bulk_matrix.R

In rnabioco/clustifyr: Classifier for Single-cell RNA-seq Using Cell Clusters

library(dplyr)
library(purrr)
library(tidyr)
library(stringr)
library(recount)

dl_recount <- function(sra_id) {
    download_study(sra_id)
    load(file.path(sra_id, "rse_gene.Rdata"))
    # no longer need to downloaded data
    unlink(sra_id, recursive = TRUE)

    rse <- scale_counts(rse_gene)
    read_counts <- assay(rse, "counts")
    gene_ids <- rownames(read_counts)
    # get gene symbols, which are stored in rowData
    id2symbol <- data_frame(
        ids = rowData(rse_gene)$gene_id,
        symbols = rowData(rse_gene)$symbol@listData
    ) %>%
        mutate(symbols = map_chr(symbols, ~ .x[1]))

    # clean up metadata into a dataframe
    mdata <- colData(rse)
    mdata_cols <- lapply(
        mdata$characteristics,
        function(x) {
            str_match(x, "^([^:]+):")[, 2]
        }
    ) %>%
        unique() %>%
        unlist()

    mdata <- data_frame(
        run = mdata$run,
        all_data = as.list(mdata$characteristics)
    ) %>%
        mutate(out = purrr::map_chr(
            all_data,
            ~ str_c(.x, collapse = "::")
        )) %>%
        tidyr::separate(out,
            sep = "::",
            into = mdata_cols
        ) %>%
        select(-all_data) %>%
        mutate_at(
            .vars = vars(-matches("run")),
            .funs = function(x) str_match(x, ": (.+)")[, 2]
        )

    # convert ids to symbols
    row_ids_to_symbols <- left_join(data_frame(ids = gene_ids),
        id2symbol,
        by = "ids"
    )

    if (length(gene_ids) != nrow(row_ids_to_symbols)) {
        warning("gene id mapping to symbols produce more or less ids")
    }

    row_ids_to_symbols <- filter(row_ids_to_symbols, !is.na(symbols))

    out_df <- read_counts %>%
        as.data.frame() %>%
        tibble::rownames_to_column("gene_id") %>%
        left_join(., row_ids_to_symbols,
            by = c("gene_id" = "ids")
        ) %>%
        dplyr::select(-gene_id) %>%
        dplyr::select(symbols, everything()) %>%
        filter(!is.na(symbols))

    out_matrix <- tidyr::gather(out_df, library, expr, -symbols) %>%
        group_by(symbols, library) %>%
        summarize(expr = sum(expr)) %>%
        tidyr::spread(library, expr) %>%
        as.data.frame() %>%
        tibble::column_to_rownames("symbols") %>%
        as.matrix()

    list(
        read_counts = out_matrix,
        meta_data = mdata
    )
}

# download
pbmc_data <- dl_recount("SRP051688")
# filter
good_libs <- filter(pbmc_data$meta_data, str_detect(time, "0"))
pbmc_data <- pbmc_data$read_counts[, good_libs$run]
# rename
new_ids <- left_join(data_frame(run = colnames(pbmc_data)),
    good_libs,
    by = "run"
) %>%
    group_by(`cell type`) %>%
    mutate(cell_id = stringr::str_c(`cell type`, " rep ", row_number())) %>%
    pull(cell_id)

colnames(pbmc_data) <- new_ids
pbmc_bulk_matrix <- pbmc_data
usethis::use_data(pbmc_bulk_matrix, compress = "xz", overwrite = TRUE)