Merge pull request #68 from umccr/oncoanalyser-sash-inputs

Support oncoanalyser and sash inputs

NAMESPACE

@@ -1,18 +1,21 @@
 # Generated by roxygen2: do not edit by hand
 
+export(abbreviate_effect)
 export(af_summary)
+export(bcftools_stats_plot)
 export(cancer_rmd)
+export(count_pieces)
 export(date_log)
+export(dragen_hrd)
+export(get_oncokb_genes)
 export(hrd_results_tabs)
 export(is_vcf)
-export(is_vcf_bpi)
 export(mkdir)
 export(pkg_exists)
 export(plot_bnd_sr_pr_tot_hist)
 export(plot_bnd_sr_pr_tot_lines)
+export(process_cnv_tsv)
 export(process_sv)
-export(purple_cnv_germ_process)
-export(purple_cnv_germ_read)
 export(purple_cnv_som_gene_process)
 export(purple_cnv_som_gene_read)
 export(purple_cnv_som_process)
@@ -21,11 +24,12 @@ export(purple_kataegis)
 export(purple_purity_read)
 export(purple_qc_read)
 export(purple_snv_vcf_read)
-export(purple_version_read)
+export(read_oncokb)
 export(session_info_kable)
 export(tsv_is_empty)
-export(umccrise_read_sv_tsv)
 export(vcf_is_empty)
+export(virusbreakend_summary_read)
+export(virusbreakend_vcf_read)
 export(write_jsongz)
 export(write_tsvgz)
 export(write_tsvjsongz)

R/oncokb.R

@@ -0,0 +1,24 @@
+#' @export
+read_oncokb <- function(x) {
+  readr::read_tsv(x) |>
+    dplyr::filter(
+      `OncoKB Annotated` == "Yes"
+    ) |>
+    dplyr::pull("Hugo Symbol")
+}
+
+#' @export
+get_oncokb_genes <- function(x, oncokb_genes) {
+  delimiters <- " ,&-"
+  delimiter_re <- paste0("[", delimiters, "]")
+
+  oncokb_genes |>
+    # Create regexes for each match, utilising delimiters for boundaries. Handles most cases where a gene symbol contains the '-' delimiter
+    purrr::map(function(n) paste0("(?<=^|", delimiter_re, ")", n, "(?=", delimiter_re, "|$)")) |>
+    # Loop with nm iterations through regex and gene symbols
+    purrr::map(function(n) stringr::str_detect(x, n) |> tibble::as_tibble_row(.name_repair="unique_quiet")) |>
+    # Combine as tibble to access dplyr::summarise and compile list of detected OncoKB gene symbols for each effect
+    dplyr::bind_rows() |>
+    dplyr::summarise(dplyr::across(dplyr::everything(), function(v) { paste0(sort(oncokb_genes[v]), collapse=", ") })) |>
+    unlist()
+}

R/oncoviral.R

@@ -0,0 +1,141 @@
+#' Read VIRUSBreakend Summary File
+#'
+#' Reads the `virusbreakend.vcf.summary.tsv` file.
+#'
+#' @param x Path to `virusbreakend.vcf.summary.tsv` file.
+#'
+#' @return List with two elements:
+#' * `tab`: Tibble containing data.
+#' * `descr`: Description of tibble columns.
+#'
+#' @examples
+#' x <- system.file("extdata/virusbreakend/virusbreakend.vcf.summary.tsv", package = "gpgr")
+#' (vb <- virusbreakend_summary_read(x))
+#' @testexamples
+#' expect_equal(colnames(vb)[ncol(vb)], "QCStatus")
+#'
+#' @export
+virusbreakend_summary_read <- function(x) {
+
+  nm <- c(
+    "taxid_genus" = "c",
+    "name_genus" = "c",
+    "reads_genus_tree" = "i",
+    "taxid_species" = "c",
+    "name_species" = "c",
+    "reads_species_tree" = "i",
+    "taxid_assigned" = "c",
+    "name_assigned" = "c",
+    "reads_assigned_tree" = "i",
+    "reads_assigned_direct" = "i",
+    "reference" = "c",
+    "reference_taxid" = "c",
+    "reference_kmer_count" = "i",
+    "alternate_kmer_count" = "i",
+    "rname" = "c",
+    "startpos" = "i",
+    "endpos" = "i",
+    "numreads" = "i",
+    "covbases" = "d",
+    "coverage" = "d",
+    "meandepth" = "d",
+    "meanbaseq" = "d",
+    "meanmapq" = "d",
+    "integrations" = "i",
+    "QCStatus" = "c"
+  )
+
+  ctypes <- paste(nm, collapse = "")
+  virusbreakend_summary <- readr::read_tsv(x, col_types = ctypes)
+
+  if (nrow(virusbreakend_summary) > 0) {
+    assertthat::assert_that(ncol(virusbreakend_summary) == length(nm))
+    assertthat::assert_that(all(colnames(virusbreakend_summary) == names(nm)))
+
+    virusbreakend_summary <- virusbreakend_summary |>
+      dplyr::select(
+        Virus="name_assigned",
+        Length="endpos",
+        Reads="numreads",
+        Coverage="coverage",
+        `Mean depth`="meandepth",
+        Intergrations="integrations",
+        QC="QCStatus",
+      )
+  }
+
+  descr <- dplyr::tribble(
+    ~Column, ~Description,
+    "Virus", "Assigned NCBI taxonomy name of viral reference",
+    "Length", "Length of viral contig",
+    "Reads", "Number of reads mapped to adjusted viral reference",
+    "Coverage", "Percentage of viral positions with at least one read mapped",
+    "Mean depth", "Mean alignment depth",
+    "Intergrations", "Number of detected integration breakpoints",
+    "QC", "QC status of viral intergrations",
+  )
+
+  list(
+    tab = virusbreakend_summary,
+    descr = descr
+  )
+}
+
+#' Read VIRUSBreakend VCF File
+#'
+#' Reads the `virusbreakend.vcf` file and selects data to present.
+#'
+#' @param x Path to `virusbreakend.vcf` file.
+#'
+#' @return List with two elements:
+#' * `tab`: Tibble containing selected data.
+#' * `descr`: Description of tibble columns.
+#'
+#' @examples
+#' x <- system.file("extdata/virusbreakend/virusbreakend.vcf", package = "gpgr")
+#' (vb <- virusbreakend_vcf_read(x))
+#' @testexamples
+#' expect_equal(colnames(vb)[ncol(vb)], "QC")
+#'
+#' @export
+virusbreakend_vcf_read <- function(x) {
+
+  d <- bedr::read.vcf(x, split.info = TRUE, verbose = FALSE)
+
+  if (nrow(d$vcf) > 0) {
+    virusbreakend_integrations <- tibble::as_tibble(d$vcf) |>
+      dplyr::select(
+          Contig="CHROM",
+          Position="POS",
+          "Fragment support"="BVF",
+          "Fragment support (unmapped)"="BUM",
+          "Softclip read support"="BSC",
+          Reference="REF",
+          Alt="ALT",
+          `Breakend ID`="ID",
+          `Mate ID`="MATEID",
+          QC="FILTER",
+      )
+  } else {
+      virusbreakend_integrations <- tibble::tibble()
+  }
+
+  descr <- dplyr::tribble(
+    ~Column, ~Description,
+    "Contig", "Name of contig",
+    "Position", "Position of breakend in contig",
+    "Breakend ID", "ID of integration breakend",
+    "Mate ID", "ID of integration breakend mate",
+    "Reference", "Reference allele",
+    "Alt", "Alternative allele",
+    "QC", "VCF filter values",
+    "Fragment support", "Total number of fragments supporting breakend",
+    "Fragment support (unmapped)", "Number of fragments supporting breakend that have one read unmapped",
+    "Softclip read support", "Number of softclipped reads supporting breakend"
+  )
+
+  list(
+    tab = virusbreakend_integrations,
+    description = descr
+  )
+}