Update as param to read_bigwig()

Now matches `rtracklayer::import.bw()` for easier migration.

R/read.r

@@ -13,19 +13,18 @@
 #' @seealso \url{https://github.com/brentp/bw-python}
 #'
 #' @examples
-#' bw <- system.file('extdata', 'test.bw', package = 'cpp11bigwig')
+#' bw <- system.file("extdata", "test.bw", package = "cpp11bigwig")
 #'
 #' read_bigwig(bw)
 #'
 #' read_bigwig(bw, chrom = "10")
 #'
 #' read_bigwig(bw, chrom = "1", start = 100, end = 130)
 #'
-#' read_bigwig(bw, as = 'gr')
+#' read_bigwig(bw, as = "GRanges")
 #'
 #' @export
 read_bigwig <- function(bwfile, chrom = NULL, start = NULL, end = NULL, as = NULL) {
-
   if (!file.exists(bwfile)) {
     stop("File does not exist: ", bwfile)
   }
@@ -34,22 +33,22 @@ read_bigwig <- function(bwfile, chrom = NULL, start = NULL, end = NULL, as = NUL
     stop("`start` and `end` must both be >= 0")
   }
 
-  if (!is.null(as) && !as %in% c("gr", "tbl")) {
-    stop("`as` must be one of 'gr' or 'tbl' (the default)")
+  if (!is.null(as) && !as %in% c("GRanges", "tbl")) {
+    stop("`as` must be one of 'GRanges' or 'tbl' (the default)")
   }
 
   res <- read_bigwig_cpp(bwfile, chrom, start, end)
 
-  if (!is.null(as) && as == 'gr') {
-    return(as_gr(res))
+  if (!is.null(as) && as == "GRanges") {
+    return(as_granges(res))
   } else {
     return(as_tibble(res))
   }
 }
 
 #' convert to GRanges
 #' @noRd
-as_gr <- function(x) {
+as_granges <- function(x) {
   GRanges(
     seqnames = x$chrom,
     ranges = IRanges(start = x$start, end = x$end),
@@ -71,15 +70,14 @@ as_gr <- function(x) {
 #' @seealso \url{https://github.com/brentp/bw-python}
 #'
 #' @examples
-#' bb <- system.file('extdata', 'test.bb', package = 'cpp11bigwig')
+#' bb <- system.file("extdata", "test.bb", package = "cpp11bigwig")
 #'
 #' read_bigbed(bb)
 #'
 #' read_bigbed(bb, chrom = "chr10")
 #'
 #' @export
 read_bigbed <- function(bbfile, chrom = NULL, start = NULL, end = NULL, convert = TRUE) {
-
   if (!file.exists(bbfile)) {
     stop("File does not exist: ", bbfile)
   }
@@ -107,12 +105,11 @@ read_bigbed <- function(bbfile, chrom = NULL, start = NULL, end = NULL, convert
 }
 
 #' @examples
-#' bb <- system.file('extdata', 'test.bb', package = 'cpp11bigwig')
+#' bb <- system.file("extdata", "test.bb", package = "cpp11bigwig")
 #' bigbed_sql_fields(bb)
 #'
 #' @noRd
 bigbed_sql_fields <- function(bbfile) {
-
   res <- bigbed_sql_cpp(bbfile)
 
   # parse the autoSql

README.Rmd

@@ -42,9 +42,9 @@ pak::pak("rnabioco/cpp11bigwig")
 ```{r}
 library(cpp11bigwig)
 
-bw <- system.file('extdata', 'test.bw', package = 'cpp11bigwig')
+bw <- system.file("extdata", "test.bw", package = "cpp11bigwig")
 read_bigwig(bw)
 
-bb <- system.file('extdata', 'test.bb', package = 'cpp11bigwig')
+bb <- system.file("extdata", "test.bb", package = "cpp11bigwig")
 read_bigbed(bb)
 ```

README.md

@@ -35,7 +35,7 @@ pak::pak("rnabioco/cpp11bigwig")
 ``` r
 library(cpp11bigwig)
 
-bw <- system.file('extdata', 'test.bw', package = 'cpp11bigwig')
+bw <- system.file("extdata", "test.bw", package = "cpp11bigwig")
 read_bigwig(bw)
 #> # A tibble: 6 × 4
 #>   chrom start   end value
@@ -47,7 +47,7 @@ read_bigwig(bw)
 #> 5 1       150   151 1.5  
 #> 6 10      200   300 2
 
-bb <- system.file('extdata', 'test.bb', package = 'cpp11bigwig')
+bb <- system.file("extdata", "test.bb", package = "cpp11bigwig")
 read_bigbed(bb)
 #> # A tibble: 3 × 12
 #>   chrom  start    end name  score strand thickStart thickEnd reserved blockCount

tests/testthat/test-read.R

@@ -1,4 +1,3 @@
-
 test_that("results have expected shape", {
   bw <- test_path("data/test.bw")
 
@@ -8,7 +7,7 @@ test_that("results have expected shape", {
   expect_true("tbl_df" %in% class(res))
 
   # interval sizes
-  expect_true(all(res$end - res$start == c(1,1,1,50,1,100)))
+  expect_true(all(res$end - res$start == c(1, 1, 1, 50, 1, 100)))
   # interval values
   expect_equal(sum(res$value), 5.5)
 
@@ -18,7 +17,7 @@ test_that("results have expected shape", {
   expect_equal(nrow(read_bigwig(bw, end = 3)), 3)
 
   # GRanges
-  res <- read_bigwig(bw, as = 'gr')
+  res <- read_bigwig(bw, as = "GRanges")
   expect_true("GRanges" %in% class(res))
 
   # bigbed
@@ -27,7 +26,6 @@ test_that("results have expected shape", {
 
   expect_equal(ncol(res), 12)
   expect_equal(nrow(res), 3)
-
 })
 
 test_that("missing file causes error", {