Merge pull request #17 from mattssca/test_branch

Test New function: cyto_ranger + improvements and new unit tests

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(bin_splitter)
+export(cyto_ranger)
 export(gene_ranger)
 export(get_gene_info)
 export(purify_chr)

R/cyto_ranger.R

@@ -0,0 +1,101 @@
+#' @title Cyto Ranger.
+#'
+#' @description This function takes a region or regions and returns the cytoband
+#' information for the region(s).
+#'
+#' @details Query a region and relevant cytoband information for the specified 
+#' region(s). This function accepts a variety of incoming regions.
+#' Either, regions can be provided as a data frame with `these_regions`.
+#' If so, the following columns must exist; chrom, start, end.
+#' This parameter (`these_regions`) also accept a region in "region" format,
+#' (i.e chr:start-end). This can be a region or a vector of characters with
+#' multiple regions. The user can also individually specify region(s) with;
+#' `qchrom` (string), `qstart` (string, or integer), and `qend` (string or integer).
+#' These parameters can also accept a vector of characters for multiple regions.
+#' The function also handles chromosome prefixes in the returned object,
+#' based on the selected `projection`.
+#'
+#' @param these_regions The region(s) to be queried. Can be a data frame with
+#' regions with the following columns; chrom, start, end.
+#' Or in a string in the following format chr:start-end.
+#' @param qchrom Query chromosome (prefixed or un-prefixed),
+#' Required if `these_regions` is not provided.
+#' @param qstart Query start position. Required if `these_regions` is not provided.
+#' @param qend Query end position. Required if `these_regions` is not provided.
+#' @param projection The desired projection you want back coordinates for.
+#' Available projections are hg38 and grch37. Default is hg38.
+#'
+#' @return A data frame with cytoband information for the specified region(s).
+#'
+#' @rawNamespace import(data.table, except = c("last", "first", "between", "transpose"))
+#' @import dplyr
+#'
+#' @export
+#'
+#' @examples
+#' #' #Example 1 - Give the function one region as a string
+#' my_region = cyto_ranger(these_regions = "chr8:127735434-127742951")
+#'
+#' #Example 2 - Give the function multiple regions as a string
+#' my_regions = cyto_ranger(these_regions = c("chr8:128747680-128753674",
+#'                                            "chr18:60790579-60987361"),
+#'                          projection = "grch37")
+#'
+#' #Example 3 - Individually specify the chromosome, start and end coordinates
+#' this_region = cyto_ranger(qchrom = "chr8",
+#'                           qstart = 127735434,
+#'                           qend = 127742951)
+#'
+#' #Example 4 - Individually specify multiple regions with the query parameters
+#' these_regions = cyto_ranger(qchrom = c("chr8", "chr18"),
+#'                             qstart = c(128747680, 60790579),
+#'                             qend = c(128753674, 60987361),
+#'                             projection = "grch37")
+#'
+cyto_ranger <- function(these_regions = NULL,
+                        qchrom = NULL,
+                        qstart = NULL,
+                        qend = NULL,
+                        projection = "hg38") {
+
+  #call helper to wrangle regions
+  region_table = BioMaesteR::purify_regions(these_regions = these_regions,
+                                            qchrom = qchrom,
+                                            qstart = qstart,
+                                            qend = qend,
+                                            projection = projection)
+
+  #deal with projections
+  if(projection == "hg38"){
+    cytobands = cytobands_hg38
+  }else if(projection == "grch37"){
+    cytobands = cytobands_grch37
+  }else{
+    stop(paste0("This function supports the following projections; hg38 and
+                grch37. The provided projection is: ", projection))
+  }
+
+  #convert to data table object
+  cytobands = as.data.table(cytobands)
+
+  #set keys
+  data.table::setkey(region_table, chrom, start, end)
+  data.table::setkey(cytobands, chrom, start, end)
+
+  #intersect regions
+  intersect = data.table::foverlaps(region_table, cytobands, nomatch = 0)
+
+  #rename columns
+  colnames(intersect)[6] = "region_start"
+  colnames(intersect)[7] = "region_end"
+  colnames(intersect)[2] = "cytoband_start"
+  colnames(intersect)[3] = "cytoband_end"
+
+  #transform object for retur
+  inter_df = as.data.frame(intersect) %>%
+    dplyr::arrange(chrom, region_start) %>%
+    dplyr::select(chrom, region_start, region_end, cytoBand, cytoband_start, cytoband_end) %>%
+    distinct(.keep_all = TRUE)
+
+  return(inter_df)
+}

R/region_ranger.R

@@ -14,7 +14,7 @@
 #' The function also handles chromosome prefixes in the returned object,
 #' based on the selected `projection`.
 #'
-#' @param these_regions these_regions The region(s) to be queried. Can be a data frame with
+#' @param these_regions The region(s) to be queried. Can be a data frame with
 #' regions with the following columns; chrom, start, end.
 #' Or in a string in the following format chr:start-end.
 #' @param qchrom Query chromosome (prefixed or un-prefixed),

tests/testthat/test_cyto_ranger.R

@@ -0,0 +1,15 @@
+library(testthat)
+
+test_that("cyto_ranger throws error with invalid projection", {
+  expect_error(cyto_ranger(these_regions = "chr8:127735434-127742951", projection = "invalid"), "This function supports the following projections")
+})
+
+test_that("cyto_ranger returns correct columns", {
+  result = cyto_ranger(these_regions = "chr8:127735434-127742951")
+  expect_equal(colnames(result), c("chrom", "region_start", "region_end", "cytoBand", "cytoband_start", "cytoband_end"))
+})
+
+test_that("cyto_ranger returns correct cytoband information", {
+  result = cyto_ranger(these_regions = "chr8:127735434-127742951")
+  expect_equal(result$cytoBand, "q24.21")
+})