1. NanoMethViz
  2. R
  3. get_cgi.R
Browse code

Added t2t exons and CGI

shians authored on 02/05/2025 02:08:29
Showing 1 changed files
R/get_cgi.R
History View file @ 28cbcef
... ... 
@@ -7,7 +7,7 @@
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 #' @return tibble (data.frame) object containing CpG islands annotation.
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 #'
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 get_cgi <- function(genome) {
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-    available_genomes <- c("hg19", "hg38", "mm10", "grcm39")
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+    available_genomes <- c("hg19", "hg38", "t2t", "mm10", "grcm39")
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     assertthat::assert_that(
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         genome %in% available_genomes,
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         msg = sprintf("genome must be one of %s", paste(available_genomes, collapse = ", "))
... ... 
@@ -17,6 +17,7 @@ get_cgi <- function(genome) {
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         genome,
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         hg19 = system.file("cgi_hg19.rds", package = "NanoMethViz", mustWork = FALSE),
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         hg38 = system.file("cgi_hg38.rds", package = "NanoMethViz", mustWork = FALSE),
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+        t2t = system.file("cgi_t2t.rds", package = "NanoMethViz", mustWork = FALSE),
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         mm10 = system.file("cgi_mm10.rds", package = "NanoMethViz", mustWork = FALSE),
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         grcm39 = system.file("cgi_GRCm39.rds", package = "NanoMethViz", mustWork = FALSE)
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     )
... ... 
@@ -44,6 +45,16 @@ get_cgi_grcm39 <- function() {
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     get_cgi("grcm39")
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 }
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+#' @rdname get_exons
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+#'
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+#' @examples
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+#' cgi_t2t <- get_cgi_t2t()
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+#'
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+#'# @export
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+get_cgi_t2t <- function() {
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+    get_cgi("t2t")
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+}
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+
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 #' @rdname get_exons
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 #'
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 #' @examples
Browse code

Ensure that all system.file calls must work

shians authored on 10/10/2024 04:13:55
Showing 1 changed files
R/get_cgi.R
History View file @ d06902a
... ... 
@@ -15,10 +15,10 @@ get_cgi <- function(genome) {
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     rds_path <- switch(
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         genome,
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-        hg19 = system.file("cgi_hg19.rds", package = "NanoMethViz"),
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-        hg38 = system.file("cgi_hg38.rds", package = "NanoMethViz"),
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-        mm10 = system.file("cgi_mm10.rds", package = "NanoMethViz"),
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-        grcm39 = system.file("cgi_GRCm39.rds", package = "NanoMethViz")
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+        hg19 = system.file("cgi_hg19.rds", package = "NanoMethViz", mustWork = FALSE),
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+        hg38 = system.file("cgi_hg38.rds", package = "NanoMethViz", mustWork = FALSE),
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+        mm10 = system.file("cgi_mm10.rds", package = "NanoMethViz", mustWork = FALSE),
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+        grcm39 = system.file("cgi_GRCm39.rds", package = "NanoMethViz", mustWork = FALSE)
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     )
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     readRDS(rds_path)
Browse code

Updated docs

shians authored on 20/08/2024 04:55:36
Showing 1 changed files
R/get_cgi.R
History View file @ d1fafaa
... ... 
@@ -2,15 +2,12 @@
2 2 
 #'
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 #' Helper functions are provided for obtaining CpG islands annotations from UCSC table browser.
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 #'
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-#' @name get_cgi
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-#' @rdname get_cgi
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+#' @keywords internal
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 #'
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 #' @return tibble (data.frame) object containing CpG islands annotation.
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 #'
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-NULL
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-
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 get_cgi <- function(genome) {
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-    available_genomes <- c("hg19", "hg38", "mm10", "GRCm39")
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+    available_genomes <- c("hg19", "hg38", "mm10", "grcm39")
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     assertthat::assert_that(
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         genome %in% available_genomes,
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         msg = sprintf("genome must be one of %s", paste(available_genomes, collapse = ", "))
... ... 
@@ -21,7 +18,7 @@ get_cgi <- function(genome) {
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         hg19 = system.file("cgi_hg19.rds", package = "NanoMethViz"),
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         hg38 = system.file("cgi_hg38.rds", package = "NanoMethViz"),
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         mm10 = system.file("cgi_mm10.rds", package = "NanoMethViz"),
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-        GRCm39 = system.file("cgi_GRCm39.rds", package = "NanoMethViz")
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+        grcm39 = system.file("cgi_GRCm39.rds", package = "NanoMethViz")
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     )
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     readRDS(rds_path)
... ... 
@@ -40,11 +37,11 @@ get_cgi_mm10 <- function() {
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 #' @rdname get_exons
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 #'
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 #' @examples
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-#' cgi_GRCm39 <- get_cgi_GRCm39()
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+#' cgi_GRCm39 <- get_cgi_grcm39()
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 #'
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 #' @export
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-get_cgi_GRCm39 <- function() {
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-    get_cgi("GRCm39")
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+get_cgi_grcm39 <- function() {
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+    get_cgi("grcm39")
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 }
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 #' @rdname get_exons
Browse code

Added helper functions for getting CpG islands annotation

shians authored on 09/05/2024 04:31:26
Showing 1 changed files
R/get_cgi.R
History View file @ cf55fa5
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,68 @@
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+#' Get CpG islands annotations
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+#'
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+#' Helper functions are provided for obtaining CpG islands annotations from UCSC table browser.
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+#'
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+#' @name get_cgi
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+#' @rdname get_cgi
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+#'
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+#' @return tibble (data.frame) object containing CpG islands annotation.
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+#'
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+NULL
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+
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+get_cgi <- function(genome) {
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+    available_genomes <- c("hg19", "hg38", "mm10", "GRCm39")
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+    assertthat::assert_that(
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+        genome %in% available_genomes,
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+        msg = sprintf("genome must be one of %s", paste(available_genomes, collapse = ", "))
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+    )
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+
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+    rds_path <- switch(
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+        genome,
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+        hg19 = system.file("cgi_hg19.rds", package = "NanoMethViz"),
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+        hg38 = system.file("cgi_hg38.rds", package = "NanoMethViz"),
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+        mm10 = system.file("cgi_mm10.rds", package = "NanoMethViz"),
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+        GRCm39 = system.file("cgi_GRCm39.rds", package = "NanoMethViz")
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+    )
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+
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+    readRDS(rds_path)
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+}
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+
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+#' @rdname get_exons
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+#'
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+#' @examples
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+#' cgi_mm10 <- get_cgi_mm10()
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+#'
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+#' @export
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+get_cgi_mm10 <- function() {
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+    get_cgi("mm10")
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+}
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+
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+#' @rdname get_exons
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+#'
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+#' @examples
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+#' cgi_GRCm39 <- get_cgi_GRCm39()
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+#'
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+#' @export
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+get_cgi_GRCm39 <- function() {
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+    get_cgi("GRCm39")
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+}
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+
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+#' @rdname get_exons
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+#'
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+#' @examples
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+#' cgi_hg19 <- get_cgi_hg19()
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+#'
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+#' @export
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+get_cgi_hg19 <- function() {
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+    get_cgi("hg19")
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+}
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+
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+#' @rdname get_exons
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+#'
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+#' @examples
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+#' cgi_hg38 <- get_cgi_hg38()
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+#'
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+#' @export
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+get_cgi_hg38 <- function() {
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+    get_cgi("hg38")
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+}