Added new exported function IsICAMSCatalog

NAMESPACE

@@ -54,6 +54,7 @@ export(GetFreebayesVAF)
 export(GetMutectVAF)
 export(GetPCAWGConsensusVAF)
 export(GetStrelkaVAF)
+export(IsICAMSCatalog)
 export(MutectVCFFilesToCatalog)
 export(MutectVCFFilesToCatalogAndPlotToPdf)
 export(MutectVCFFilesToZipFile)

NEWS.md

@@ -3,6 +3,9 @@
 * Updated `catalog.row.order$ID166` and `catalog.row.headers$ID166` 
 for genic-intergenic indel catalog (ID166).
 
+## Added
+* Added new exported function `IsICAMSCatalog`.
+
 # 3.0.4
 ## Changed
 * Changed the legend of ID166 plot from `Nongenic region` to `Intergenic region`.

R/infer_catalog_format.R

@@ -71,6 +71,60 @@ InferCatalogClassString <- function(object) {
   return(paste0(prefix, "Catalog"))
 }
 
+#' Check whether an R object contains one of the ICAMS catalog classes 
+#'
+#' @param object An R object.
+#'
+#' @return A logical value.
+#' 
+#' @export
+#'
+#' @examples
+#' # Create a matrix with all values being 1
+#' object <- matrix(1, nrow = 96, ncol = 1, 
+#'                  dimnames = list(catalog.row.order$SBS96))
+#' IsICAMSCatalog(object) # FALSE
+#' 
+#' # Use as.catalog to add class attribute to object
+#' catalog <- as.catalog(object)
+#' IsICAMSCatalog(catalog) # TRUE      
+IsICAMSCatalog <- function(object) {
+  supported.num.rows <- 
+    c(96, 192, 1536, 78, 136, 144, 83, 166, 1697)
+  supported.type <- 
+    c(paste0("SBS", c(96, 192, 1536)),
+      paste0("DBS", c(78, 136, 144)),
+      "ID", "ID166", "COMPOSITE")
+  supported.classes <-
+    paste0(supported.type, "Catalog")
+
+  # Change "IDCatalog" class to "IndelCatalog"
+  supported.classes[supported.classes == "IDCatalog"] <-
+    "IndelCatalog"
+
+  if (!nrow(object) %in% supported.num.rows) {
+    return(FALSE)
+  } 
+
+  if (!inherits(x = object, what = supported.classes)) {
+    return(FALSE)
+  } 
+
+  if (!is.null(rownames(object))) {
+    index <- which(nrow(object) == supported.num.rows)
+    type <- supported.type[index]
+    if (all(rownames(object) == ICAMS::catalog.row.order[[type]])) {
+      return(TRUE)
+    } else {
+      message("The rownames of the input object do not match the catalog row ",
+              "order used in ICAMS exactly. See ICAMS::catalog.row.order for details")
+      return(FALSE)
+    }
+  }
+
+  return(TRUE)
+}
+
 
 
 ## Convert external catalog files with 96 rows into ICAMS internal catalog format.

tests/testthat/test_IsICAMSCatalog.R

@@ -0,0 +1,40 @@
+context("Test IsICAMSCatalog function")
+
+test_that("IsICAMSCatalog function", {
+dir <- c(system.file("extdata/Mutect-vcf",
+                     package = "ICAMS"))
+catalogs <-
+  VCFsToZipFile(dir,
+                zipfile = file.path(tempdir(), "test.zip"),
+                ref.genome = "hg19",
+                variant.caller = "mutect",
+                region = "genome",
+                base.filename = "Mutect")
+cat.sbs96 <- catalogs$catSBS96
+dim(cat.sbs96)
+expect_true(IsICAMSCatalog(cat.sbs96))
+
+# Test subsetting the catalog
+test <- cat.sbs96[, 1, drop = FALSE]
+dim(test)
+expect_true(IsICAMSCatalog(test)) 
+
+# Test a matrix with incorrect number of rows
+mat1 <- matrix(data = 1, nrow = 97)
+expect_false(IsICAMSCatalog(mat1)) 
+
+# Test a matrix with correct number of rows but incorrect class
+mat2 <- matrix(data = 1, nrow = 96)
+expect_false(IsICAMSCatalog(mat2)) 
+
+# Test a matrix with correct number of rows and class, but incorrect
+# rownames
+mat3 <- matrix(data = 1, nrow = 96)
+mat3 <- as.catalog(mat3, infer.rownames = TRUE)
+rownames(mat3) <- paste0("test", 1:96)
+
+result <- 
+  expect_message(IsICAMSCatalog(mat3), 
+                 "The rownames of the input object do not match the catalog row order used in ICAMS exactly.") 
+expect_false(result)
+})