Add the new signature and update reference

Add the PCAWG and TCGA signature matrix from BIB 2023. The new names of  them are "CNS_TCGA176" and "CNS_PCAWG176" to preventing confuse of "CNS_TCGA" from Nature2022. Update the description of function "sig_db"

DESCRIPTION

@@ -82,7 +82,7 @@ Suggests:
     roxygen2,
     scales,
     synchronicity,
-    testthat,
+    testthat (>= 3.0.0),
     tibble,
     UCSCXenaTools
 LinkingTo: 
@@ -95,3 +95,4 @@ LazyData: true
 Roxygen: list(markdown = TRUE, roclets = c("collate", "namespace", "rd",
     "roxytest::testthat_roclet"))
 RoxygenNote: 7.2.3
+Config/testthat/edition: 3

R/get_sig_db.R

@@ -11,16 +11,17 @@
 #' - SBS and RS (rearrangement) signatures from Nik lab 2020 Nature Cancer paper.
 #' - RS signatures from BRCA560 and USARC cohorts.
 #' - Copy number signatures from USARC cohort and TCGA.
+#' - Copy number signatures from Liu lab 2023. It supports both PCAWG and TCGA cohort.
 #' @inheritParams get_sig_similarity
 #'
 #' @return a `list`.
 #' @export
 #' @seealso [get_sig_similarity], [sig_fit] and [show_cosmic_sig_profile].
 #' @references
-#' - Steele, Christopher D., et al. "Signatures of copy number alterations in human cancer." bioRxiv (2021).
+#' - Steele, Christopher D., et al. "Signatures of copy number alterations in human cancer." Nature 606.7916 (2022): 984-991.
 #' - Alexandrov, Ludmil B., et al. "The repertoire of mutational signatures in human cancer." Nature 578.7793 (2020): 94-101.
 #' - Steele, Christopher D., et al. "Undifferentiated sarcomas develop through distinct evolutionary pathways." Cancer Cell 35.3 (2019): 441-456.
-#'
+#' - Ziyu Tao, et al. "The repertoire of copy number alteration signatures in human cancer." Briefings in Bioinformatics (2023): bbad053.
 #' @examples
 #' s1 <- get_sig_db()
 #' s2 <- get_sig_db("SBS")
@@ -33,6 +34,8 @@
 #' s9 <- get_sig_db("RS_Nik_lab")
 #' s10 <- get_sig_db("CNS_USARC")
 #' s11 <- get_sig_db("CNS_TCGA")
+#' s12 <- get_sig_db("CNS_TCGA176")
+#' s13 <- get_sig_db("CNS_PCAWG176")
 #' s1
 #' s2
 #' s3
@@ -44,6 +47,8 @@
 #' s9
 #' s10
 #' s11
+#' s12
+#' s13
 #' @testexamples
 #' expect_is(s1, "list")
 #' expect_is(s2, "list")
@@ -56,6 +61,8 @@
 #' expect_is(s9, "list")
 #' expect_is(s10, "list")
 #' expect_is(s11, "list")
+#' expect_is(s12, "list")
+#' expect_is(s13, "list")
 get_sig_db <- function(sig_db = "legacy") {
   db_file <- switch(sig_db,
     legacy = system.file("extdata", "legacy_signatures.RDs",
@@ -88,6 +95,12 @@ get_sig_db <- function(sig_db = "legacy") {
     CNS_TCGA = system.file("extdata", "CNS_signatures_TCGA.rds",
                             package = "sigminer", mustWork = TRUE
     ),
+    CNS_TCGA176 = system.file("extdata","CNS_signatures_TCGA176.rds",
+                           package = "sigminer", mustWork = TRUE
+    ),
+    CNS_PCAWG176 = system.file("extdata", "CNS_signatures_PCAWG176.rds",
+                           package = "sigminer", mustWork = TRUE
+    ),
     DBS = system.file("extdata", "DBS_signatures.rds",
       package = "sigminer", mustWork = TRUE
     ),

R/get_sig_similarity.R

@@ -23,7 +23,8 @@
 #' "SBS_Nik_lab", "RS_Nik_lab" to refer reference signatures from
 #' Degasperi, Andrea, et al. (2020) (reference #2);
 #' "RS_BRCA560", "RS_USARC" to reference signatures from BRCA560 and USARC cohorts;
-#' "CNS_USARC" (40 categories), "CNS_TCGA" (48 categories) to reference copy number signatures from USARC cohort and TCGA.
+#' "CNS_USARC" (40 categories), "CNS_TCGA" (48 categories) to reference copy number signatures from USARC cohort and TCGA;
+#' "CNS_TCGA176" (176 categories) and "CNS_PCAWG176" (176 categories) to reference copy number signatures from PCAWG and TCGA separately.
 #' **UPDATE**, the latest version of reference version can be automatically
 #' downloaded and loaded from <https://cancer.sanger.ac.uk/signatures/downloads/>
 #' when a option with `latest_` prefix is specified (e.g. "latest_SBS_GRCh37").
@@ -56,7 +57,7 @@
 #'
 #' Nik-Zainal, Serena, et al. "Landscape of somatic mutations in 560 breast cancer whole-genome sequences." Nature 534.7605 (2016): 47-54.
 #'
-#' Steele, Christopher D., et al. "Signatures of copy number alterations in human cancer." bioRxiv (2021).
+#' Steele, Christopher D., et al. "Signatures of copy number alterations in human cancer." Nature 606.7916 (2022): 984-991.
 #' @return a `list` containing smilarities, aetiologies if available, best match and RSS.
 #' @export
 #'
@@ -102,7 +103,9 @@ get_sig_similarity <- function(Signature, Ref = NULL,
                                sig_db = c(
                                  "SBS", "legacy", "DBS", "ID", "TSB",
                                  "SBS_Nik_lab", "RS_Nik_lab",
-                                 "RS_BRCA560", "RS_USARC", "CNS_USARC", "CNS_TCGA",
+                                 "RS_BRCA560", "RS_USARC",
+                                 "CNS_USARC", "CNS_TCGA",
+                                 "CNS_TCGA176","CNS_PCAWG176",
                                  "SBS_hg19", "SBS_hg38", "SBS_mm9", "SBS_mm10",
                                  "DBS_hg19", "DBS_hg38", "DBS_mm9", "DBS_mm10",
                                  "SBS_Nik_lab_Organ", "RS_Nik_lab_Organ",

R/sig_fit.R

@@ -100,7 +100,9 @@ sig_fit <- function(catalogue_matrix,
                     sig_db = c(
                       "legacy", "SBS", "DBS", "ID", "TSB",
                       "SBS_Nik_lab", "RS_Nik_lab",
-                      "RS_BRCA560", "RS_USARC", "CNS_USARC", "CNS_TCGA",
+                      "RS_BRCA560", "RS_USARC",
+                      "CNS_USARC", "CNS_TCGA",
+                      "CNS_TCGA176","CNS_PCAWG176",
                       "SBS_hg19", "SBS_hg38", "SBS_mm9", "SBS_mm10",
                       "DBS_hg19", "DBS_hg38", "DBS_mm9", "DBS_mm10",
                       "SBS_Nik_lab_Organ", "RS_Nik_lab_Organ",