New helper and hot fixes

NAMESPACE

@@ -2,6 +2,7 @@
 
 export(gene_ranger)
 export(get_gene_info)
+export(purify_chr)
 export(purify_regions)
 export(region_ranger)
 import(data.table, except = c("last", "first", "between", "transpose"))

R/purify_chr.R

@@ -0,0 +1,55 @@
+#' @title Purify Chromosomes.
+#'
+#' @description Helper function for dealing with chromosome prefixes based on 
+#' the selected projection.
+#'
+#' @details This function accepts a data frame with a column to check for
+#' prefixes. The function will add or remove prefixes based on the selected
+#' projection. This function expects a column named "chrom" to be in the 
+#' incoming data frame.
+#'
+#' @param projection Required parameter, needed to determine if chromosomes 
+#' should be prefixed or not.
+#' @param incoming_table Required parameter, a data frame to check for prefixes.
+#'
+#' @return A data frame with the same columns as the incoming data frame, but
+#' with the prefixes added or removed based on the selected projection.
+#'
+#' @import dplyr stringr
+#'
+#' @export
+#'
+#' @examples
+#' #Example 1 - Add prefixes to a data frame
+#' my_data = data.frame(chrom = c("1", "2", "3"))
+#' my_data = purify_chr(projection = "hg38", incoming_table = my_data)
+#'
+purify_chr <- function(projection = NULL,
+                       incoming_table = NULL) {
+
+  #checks
+  if(is.null(projection)){
+    stop("You must provide a valid projection. 
+         Available projections are hg38 and grch37.")
+  }
+
+  if(is.null(incoming_table)){
+    stop("You must provide a data table with `incoming_table`.")
+  }
+
+    #deal with prefixes
+  if(projection == "hg38"){
+    if(all(!str_detect(incoming_table$chrom, "chr"))){
+      incoming_table =  dplyr::mutate(incoming_table, chrom = paste0("chr", chrom))
+    }
+  }else if(projection == "grch37"){
+    if(all(str_detect(incoming_table$chrom, "chr"))){
+      incoming_table = dplyr::mutate(incoming_table, chrom = gsub("chr", "", chrom))
+    }
+  }else{
+    stop(paste0("This function supports the following projections; hg38 and
+                grch37. The provided projection is: ", projection))
+  }
+
+  return(incoming_table)
+}

R/purify_regions.R

@@ -1,6 +1,6 @@
 #' @title Purify Regions.
 #'
-#' @description Helper function for cleaning and standaradize regions.
+#' @description Helper function for cleaning and standardize regions.
 #'
 #' @details This function accepts a variety of incoming regions.
 #' Either, regions can be provided as a data frame with `these_regions`.
@@ -103,20 +103,9 @@ purify_regions <- function(these_regions = NULL,
          `qchrom`, `qstart`, and `qend`")
   }
 
-  #TODO: Turn this into a helper function:
-  #deal with chr prefixes based on selected projection
-  if(projection == "hg38"){
-    if(all(!str_detect(region_table$chrom, "chr"))){
-      region_table =  dplyr::mutate(region_table, chrom = paste0("chr", chrom))
-    }
-  }else if(projection == "grch37"){
-    if(all(str_detect(region_table$chrom, "chr"))){
-      region_table = dplyr::mutate(region_table, chrom = gsub("chr", "", chrom))
-    }
-  }else{
-    stop(paste0("This function supports the following projections; hg38 and
-                grch37. The provided projection is: ", projection))
-  }
+  #run helper function to deal with prefixes
+  region_table = purify_chr(projection = projection,
+                            incoming_table = region_table)
 
   #enforce data types
   region_table$chrom = as.character(region_table$chrom)

tests/testthat/test-get_gene_infoR.R → tests/testthat/test-get_gene_info.R

@@ -34,3 +34,8 @@ test_that("Expected to fail", {
   expect_error(get_gene_info(these_genes = "MYC",
                              projection = "hg19"))
 })
+
+
+test_that("Check the type of the return", {
+  expect_true(is.data.frame(get_gene_info(these_genes = c("BCL2", "MYC"))))
+})