R/export_markers.R

In campsj/scTools: Tools to help with analysis of single-cell transcriptome datasets

#' Filter and save markers
#'
#' Filters marker genes based on padj and k and saves them as a csv file
#' @param sce_object A single cell experiment object
#' @param k number of clusters
#' @param padj Adjusted p value
#' @param auroc Area Under Receiving Operating Curve
#' @param folder Folder where to export the file to
#' @param filename Name for exported csv file
#' @return csv file
#' @export

export_markers <- function(sce_object, k, padj = 0.01, auroc = 0.85, folder, filename) {
  #require(c("SC3", "lazyeval", "dplyr", "rlang"))

  k_clusts <- paste0("sc3_", k, "_markers_clusts", sep = "")
  k_auroc <- paste0("sc3_", k, "_markers_auroc", sep = "")
  k_padj <- paste0("sc3_", k, "_markers_padj", sep = "")

  #sc3_plot_markers(sce_object, k = k, show_pdata = TRUE)

  sce_object %>%
    rowData() %>%
    as_tibble() %>%
    #group_by_(k_clusts) %>%
    filter_(interp(~ a < x & b > y,
                   a = as.name(k_padj),
                   b = as.name(k_auroc),
                   x = padj,
                   y = auroc)) %>%
    select_("mgi_symbol", "ensembl_gene_id", "log10_mean_counts", k_auroc, k_clusts, k_padj) %>%
    arrange_(.dots = c(k_clusts, k_padj)) %>%
    write.csv(paste0(folder, "/", filename, ".csv"))
}