#299 Add reference signatures data from Nik lab work

data-raw/Nature-Cancer-Sigs.R

@@ -0,0 +1,85 @@
+## code to prepare `Nature-Cancer-Sigs` dataset goes here
+# Data form Nik-Zainal lab work
+
+library(readxl)
+library(magrittr)
+
+s1 <- read_excel("data-raw/NC-Ref-Sigs.xlsx")
+s2 <- read_excel("data-raw/NC-Ref-Sigs.xlsx", sheet = 2)
+s3 <- read_excel("data-raw/NC-Ref-Sigs.xlsx", sheet = 3)
+s4 <- read_excel("data-raw/NC-Ref-Sigs.xlsx", sheet = 4)
+
+
+# S1 and S2 ---------------------------------------------------------------
+
+s1 <- s1 %>% tibble::column_to_rownames("Type") %>% as.matrix()
+s1_names <- colnames(s1)
+s1_map <- stringr::str_split(s1_names, pattern = " ", simplify = T) %>%
+  as.data.frame() %>%
+  dplyr::mutate(V2 = stringr::str_remove(V2, "\\("),
+                V2 = stringr::str_remove(V2, "\\)"),
+                V2 = stringr::str_remove(V2, "^[^_]+_"),
+                V2 = stringr::str_remove(V2, "SoftTissue_"),
+                V2 = stringr::str_remove(V2, "neck_"),
+                V2 = stringr::str_replace_all(V2, "_", ","))
+
+colnames(s1) <- s1_map$V1
+
+SBS_Nik_lab_Organ <- list(
+  db = s1,
+  aetiology = s1_map %>% tibble::column_to_rownames("V1") %>% setNames("aetiology"),
+  date = "2020/10/20"
+)
+
+saveRDS(SBS_Nik_lab_Organ, file = "inst/extdata/SBS_signatures_Nik_lab_Organ.rds")
+
+s2 <- s2 %>% tibble::column_to_rownames("Type") %>% as.matrix()
+s2_names <- colnames(s2)
+s2_map <- stringr::str_split(s2_names, pattern = " ", simplify = T) %>%
+  as.data.frame() %>%
+  dplyr::mutate(V2 = stringr::str_remove(V2, "\\("),
+                V2 = stringr::str_remove(V2, "\\)"),
+                V2 = stringr::str_remove(V2, "^[^_]+_"),
+                V2 = stringr::str_remove(V2, "SoftTissue_"),
+                V2 = stringr::str_remove(V2, "neck_"),
+                V2 = stringr::str_replace_all(V2, "_", ","))
+
+colnames(s2) <- s2_map$V1
+
+RS_Nik_lab_Organ <- list(
+  db = s2,
+  aetiology = s2_map %>% tibble::column_to_rownames("V1") %>% setNames("aetiology"),
+  date = "2020/10/20"
+)
+
+saveRDS(RS_Nik_lab_Organ, file = "inst/extdata/RS_signatures_Nik_lab_Organ.rds")
+
+# S3 and S4 ---------------------------------------------------------------
+
+s3 <- s3 %>% tibble::column_to_rownames("Type") %>% as.matrix()
+colnames(s3) <- gsub("\\.", "_", colnames(s3))
+
+SBS_Nik_lab <- list(
+  db = s3,
+  aetiology = data.frame(
+    V1 = colnames(s3),
+    V2 = "See COSMIC signatures with same ID or check Nik-Zainal lab Nature Cancer paper "
+  ) %>% tibble::column_to_rownames("V1") %>% setNames("aetiology"),
+  date = "2020/10/20"
+)
+
+saveRDS(SBS_Nik_lab, file = "inst/extdata/SBS_signatures_Nik_lab.rds")
+
+s4 <- s4 %>% tibble::column_to_rownames("Type") %>% as.matrix()
+colnames(s4) <- gsub("\\.", "_", colnames(s4))
+
+RS_Nik_lab <- list(
+  db = s4,
+  aetiology = data.frame(
+    V1 = colnames(s4),
+    V2 = "See COSMIC signatures with same ID or check Nik-Zainal lab Nature Cancer paper "
+  ) %>% tibble::column_to_rownames("V1") %>% setNames("aetiology"),
+  date = "2020/10/20"
+)
+
+saveRDS(RS_Nik_lab, file = "inst/extdata/RS_signatures_Nik_lab.rds")