covert docs to markdown. (#231)

Author: jayhesselberth

DESCRIPTION

@@ -39,3 +39,4 @@ VignetteBuilder: knitr
 RoxygenNote: 6.0.1
 URL: http://github.com/rnabioco/valr/
 BugReports: https://github.com/rnabioco/valr/issues
+Roxygen: list(markdown = TRUE)

R/bed12_to_exons.r

@@ -1,10 +1,10 @@
 #' Convert BED12 to individual exons in BED6.
 #'
-#' After conversion to BED6 format, the \code{score} column contains the exon
-#' number, with respect to strand (i.e., the first exon for \code{-} strand
+#' After conversion to BED6 format, the `score` column contains the exon
+#' number, with respect to strand (i.e., the first exon for `-` strand
 #' genes will have larger start and end coordinates).
 #'
-#' @param x \code{\link{tbl_interval}}
+#' @param x [tbl_interval()]
 #' @family utilities
 #'
 #' @examples

R/bed_absdist.r

@@ -1,25 +1,25 @@
 #' Compute absolute distances between intervals.
 #'
-#' Computes the absolute distance between the midpoints of \code{x} intervals and
-#' the closest midpoints of \code{y} intervals.
+#' Computes the absolute distance between the midpoints of `x` intervals and
+#' the closest midpoints of `y` intervals.
 #'
 #' @details Absolute distances are scaled by the inter-reference gap for the
-#'   chromosome as follows. For \code{Q} query points and \code{R} reference
-#'   points on a chromosome, scale the distance for each query point \code{i} to
+#'   chromosome as follows. For `Q` query points and `R` reference
+#'   points on a chromosome, scale the distance for each query point `i` to
 #'   the closest reference point by the inter-reference gap for each chromosome.
-#'   If an \code{x} interval has no matching \code{y} chromosome,
-#'   \code{.absdist} is \code{NA}.
+#'   If an `x` interval has no matching `y` chromosome,
+#'   `.absdist` is `NA`.
 #'
 #'   \deqn{d_i(x,y) = min_k(|q_i - r_k|)\frac{R}{Length\ of\ chromosome}}
 #'
-#'   Both absolute and scaled distances are reported as \code{.absdist} and
-#'   \code{.absdist_scaled}.
+#'   Both absolute and scaled distances are reported as `.absdist` and
+#'   `.absdist_scaled`.
 #'
-#' @param x \code{\link{tbl_interval}}
-#' @param y \code{\link{tbl_interval}}
-#' @param genome \code{\link{tbl_genome}}
+#' @param x [tbl_interval()]
+#' @param y [tbl_interval()]
+#' @param genome [tbl_genome()]
 #'
-#' @return \code{\link{tbl_interval}} with \code{.absdist} and \code{.absdist_scaled}
+#' @return [tbl_interval()] with `.absdist` and `.absdist_scaled`
 #'   columns.
 #'
 #' @template stats

R/bed_closest.r

@@ -1,17 +1,15 @@
 #' Identify closest intervals.
 #'
-#' @param x \code{\link{tbl_interval}}
-#' @param y \code{\link{tbl_interval}}
+#' @param x [tbl_interval()]
+#' @param y [tbl_interval()]
 #' @param overlap report overlapping intervals
 #' @param suffix colname suffixes in output
 #'
 #' @template groups
 #'
-#' @return \code{\link{tbl_interval}} with additional columns:
-#'   \itemize{
-#'     \item{\code{.dist}}{ distance to closest interval, negative distances denote upstream intervals}
-#'     \item{\code{.overlap}}{ overlap with closest interval}
-#'   }
+#' @return [tbl_interval()] with additional columns:
+#'   - `.dist` distance to closest interval, negative distances denote upstream intervals
+#'   - `.overlap` overlap with closest interval
 #'
 #' @family multiple set operations
 #' @seealso \url{http://bedtools.readthedocs.io/en/latest/content/tools/closest.html}
@@ -50,14 +48,14 @@
 #'
 #' # Report distance based on strand
 #' x <- trbl_interval(
-#'   ~chrom,   ~start,    ~end, ~name, ~score, ~strand,
-#'   "chr1",	10,	20,	"a",	1,	"-"
+#'   ~chrom, ~start, ~end, ~name, ~score, ~strand,
+#'   "chr1", 10,	   20,   "a",   1,      "-"
 #' )
 #'
 #' y <- trbl_interval(
-#'   ~chrom,   ~start,    ~end, ~name, ~score, ~strand,
-#'   "chr1",	8,	9,	"b",	1,	"+",
-#'   "chr1",	21,	22,	"b",	1, "-"
+#'   ~chrom, ~start, ~end, ~name, ~score, ~strand,
+#'   "chr1", 8,	     9,	   "b",   1,      "+",
+#'   "chr1", 21,	   22,	 "b",   1,      "-"
 #' )
 #'
 #' res <- bed_closest(x, y)

R/bed_cluster.r

@@ -1,15 +1,15 @@
 #' Cluster neighboring intervals.
 #'
-#' Output contains an \code{.id} column that can be used in downstream grouping
-#' operations. Default \code{max_dist = 0} means that both overlapping and
+#' Output contains an `.id` column that can be used in downstream grouping
+#' operations. Default `max_dist = 0` means that both overlapping and
 #' book-ended intervals will be clustered.
 #'
-#' @param x \code{\link{tbl_interval}}
+#' @param x [tbl_interval()]
 #' @param max_dist maximum distance between clustered intervals.
 #'
 #' @template groups
 #'
-#' @return \code{\link{tbl_interval}} with \code{.id} column for clustered intervals.
+#' @return [tbl_interval()] with `.id` column for clustered intervals.
 #'
 #' @family single set operations
 #' @seealso

R/bed_complement.r

@@ -1,11 +1,11 @@
 #' Identify intervals in a genome not covered by a query.
 #'
-#' @param x \code{\link{tbl_interval}}
-#' @param genome \code{\link{tbl_genome}}
+#' @param x [tbl_interval()]
+#' @param genome [tbl_genome()]
 #'
 #' @family single set operations
 #'
-#' @return \code{\link{tbl_interval}}
+#' @return [tbl_interval()]
 #'
 #' @examples
 #' x <- trbl_interval(

R/bed_coverage.R

@@ -1,7 +1,7 @@
 #' Compute coverage of intervals.
 #'
-#' @param x \code{\link{tbl_interval}}
-#' @param y \code{\link{tbl_interval}}
+#' @param x [tbl_interval()]
+#' @param y [tbl_interval()]
 #' @param ... extra arguments (not used)
 #'
 #' @note Book-ended intervals are counted as overlapping.
@@ -10,14 +10,12 @@
 #'
 #' @family multiple set operations
 #'
-#' @return \code{x} \code{\link{tbl_interval}} with the following additional
+#' @return `x` [tbl_interval()] with the following additional
 #'   columns:
-#' \itemize{
-#'   \item{\code{.ints}}{ number of x intersections}
-#'   \item{\code{.cov}}{ per-base coverage of x intervals}
-#'   \item{\code{.len}}{ total length of y intervals covered by x intervals}
-#'   \item{\code{.frac}}{ .len scaled by total of y intervals}
-#'   }
+#'   - `.ints` number of x intersections
+#'   - `.cov` per-base coverage of x intervals
+#'   - `.len` total length of y intervals covered by x intervals
+#'   - `.frac` `.len` scaled by total of y intervals
 #
 #' @examples
 #' x <- trbl_interval(

R/bed_fisher.r

@@ -1,18 +1,18 @@
 #' Fisher's test on number of shared and unique intervals.
 #'
-#' Borrows from the \code{BEDtools} implementation.
+#' Borrows from the `BEDtools` implementation.
 #'
-#' @param x \code{\link{tbl_interval}}
-#' @param y \code{\link{tbl_interval}}
-#' @param genome \code{\link{tbl_genome}}
+#' @param x [tbl_interval()]
+#' @param y [tbl_interval()]
+#' @param genome [tbl_genome()]
 #'
 #' @template stats
 #'
 #' @family interval statistics
 #' @seealso
 #'   \url{http://bedtools.readthedocs.org/en/latest/content/tools/fisher.html}
 #'
-#' @return \code{tbl_interval}
+#' @return `tbl_interval`
 #'
 #' @examples
 #' x <- trbl_interval(

R/bed_flank.r

@@ -1,16 +1,16 @@
 #' Create flanking intervals from input intervals.
 #'
-#' @param x \code{\link{tbl_interval}}
-#' @param genome \code{\link{tbl_genome}}
+#' @param x [tbl_interval()]
+#' @param genome [tbl_genome()]
 #' @param both number of bases on both sizes
 #' @param left number of bases on left side
 #' @param right number of bases on right side
 #' @param fraction define flanks based on fraction of interval length
-#' @param strand define \code{left} and \code{right} based on strand
+#' @param strand define `left` and `right` based on strand
 #' @param trim adjust coordinates for out-of-bounds intervals
 #' @param ... extra arguments (not used)
 #'
-#' @return \code{\link{tbl_interval}}
+#' @return [tbl_interval()]
 #'
 #' @family single set operations
 #' @seealso

R/bed_glyph.r

@@ -6,7 +6,7 @@
 #' @param label column name to use for label values. should be present in the
 #'   result of the call.
 #'
-#' @return \code{\link[ggplot2]{ggplot}}
+#' @return [ggplot2::ggplot()]
 #'
 #' @examples
 #' x <- trbl_interval(

R/bed_intersect.r

@@ -1,24 +1,24 @@
 #' Identify intersecting intervals.
 #'
-#' Report intersecting intervals from \code{x} and \code{y} tbls. Book-ended
-#' intervals (or "touching" intervals) have \code{.overlap} values of \code{0})
+#' Report intersecting intervals from `x` and `y` tbls. Book-ended
+#' intervals (or "touching" intervals) have `.overlap` values of `0`)
 #' in the output.
 #'
-#' @param x \code{\link{tbl_interval}}
-#' @param ... single y  \code{\link{tbl_interval}}, multiple y \code{\link{tbl_interval}s}
-#'                   or a list of y  \code{tbl_intervals}
-#' @param invert report \code{x} intervals not in \code{y}
+#' @param x [tbl_interval()]
+#' @param ... single y  [tbl_interval()], multiple y \code{\link{tbl_interval}s}
+#'                   or a list of y  `tbl_intervals`
+#' @param invert report `x` intervals not in `y`
 #' @param suffix colname suffixes in output
 #'
-#' @return \code{\link{tbl_interval}} with original columns from \code{x} and \code{y},
-#'   suffixed with \code{.x} and \code{.y}, and a new \code{.overlap} column
+#' @return [tbl_interval()] with original columns from `x` and `y`,
+#'   suffixed with `.x` and `.y`, and a new `.overlap` column
 #'   with the extent of overlap for the intersecting intervals.
 #'
-#'   If  multiple \code{y} tbls are supplied, then an additional column \code{.source} will
+#'   If  multiple `y` tbls are supplied, then an additional column `.source` will
 #'   be reported that contains the variable names associated with each interval. All original
-#'   columns from the y tbls will be suffixed with \code{.y} in the output.
-#'   If named tbls are supplied to \code{...} (i.e \code{a = y, b = z} or
-#'    \code{list(a = y, b = z)}), then the supplied names will be reported instead
+#'   columns from the y tbls will be suffixed with `.y` in the output.
+#'   If named tbls are supplied to `...` (i.e `a = y, b = z` or
+#'    `list(a = y, b = z)`), then the supplied names will be reported instead
 #'   of the variable names (see examples).
 #'
 #'

R/bed_jaccard.r

@@ -1,26 +1,24 @@
 #' Calculate jaccard statistics on two sets of intervals.
 #'
-#' @details \code{bed_jaccard()} quantifies the extent of overlap between to sets of
-#' intervals. The Jaccard statistic takes values of \code{[0,1]} and is measured as:
+#' @details `bed_jaccard()` quantifies the extent of overlap between to sets of
+#' intervals. The Jaccard statistic takes values of `[0,1]` and is measured as:
 #'
 #' \deqn{ J(x,y) = \frac{\mid x \bigcap y \mid}
 #'                      {\mid x \bigcup y \mid} =
 #'                 \frac{\mid x \bigcap y \mid}
 #'                      {\mid x \mid + \mid y \mid - \mid x \bigcap y \mid} }
 #'
-#' @param x \code{\link{tbl_interval}}
-#' @param y \code{\link{tbl_interval}}
+#' @param x [tbl_interval()]
+#' @param y [tbl_interval()]
 #'
 #' @template stats
 #'
 #' @family interval statistics
-#' @return \code{\link{tbl_interval}} with the following columns:
-#'   \itemize{
-#'     \item{\code{len_i}}{ length of the intersection}
-#'     \item{\code{len_u}}{ length of the union}
-#'     \item{\code{jaccard}}{ jaccard statistic}
-#'     \item{\code{n_int}}{ number of intersecting intervals between x and y}
-#'     }
+#' @return [tbl_interval()] with the following columns:
+#'   - `len_i` length of the intersection
+#'   - `len_u` length of the union
+#'   - `jaccard` jaccard statistic
+#'   - `n_int` number of intersecting intervals between x and y
 #'
 #' @seealso
 #'   \url{http://bedtools.readthedocs.org/en/latest/content/tools/jaccard.html}

R/bed_makewindows.r

@@ -1,18 +1,18 @@
 #' Divide intervals into new sub-intervals ("windows").
 #'
-#' @param x \code{\link{tbl_interval}}
-#' @param genome \code{\link{tbl_genome}}
+#' @param x [tbl_interval()]
+#' @param genome [tbl_genome()]
 #' @param win_size divide intervals into fixed-size windows
 #' @param step_size size to step before next window
 #' @param num_win divide intervals to fixed number of windows
 #' @param reverse reverse window numbers
 #'
-#' @note The \code{name} and \code{.win_id} columns can be used to create new
+#' @note The `name` and `.win_id` columns can be used to create new
 #'   interval names (see 'namenum' example below) or in subsequent
-#'   \code{group_by} operations (see vignette).
+#'   `group_by` operations (see vignette).
 #'
 #' @family utilities
-#' @return \code{\link{tbl_interval}} with \code{.win_id} column that contains a numeric
+#' @return [tbl_interval()] with `.win_id` column that contains a numeric
 #'   identifier for the window.
 #'
 #' @examples

R/bed_map.r

@@ -1,20 +1,20 @@
 #' Calculate summaries and statistics from overlapping intervals.
 #'
-#' Used to apply functions like \code{\link{min}()}, \code{\link{count}()},
-#' \code{\link{concat}()} to intersecting intervals. Book-ended intervals are
+#' Used to apply functions like [min()], [count()],
+#' [concat()] to intersecting intervals. Book-ended intervals are
 #' not reported by default, but can be included by setting \code{min_overlap =
 #' 0}.
 #'
-#' @param x \code{\link{tbl_interval}}
-#' @param y  \code{\link{tbl_interval}}
-#' @param invert report \code{x} intervals not in \code{y}
+#' @param x [tbl_interval()]
+#' @param y  [tbl_interval()]
+#' @param invert report `x` intervals not in `y`
 #' @param suffix colname suffixes in output
 #' @param min_overlap minimum overlap for intervals.
 #' @param ... name-value pairs specifying colnames and expressions to apply
 #'
 #' @template groups
 #'
-#' @return \code{\link{tbl_interval}}
+#' @return [tbl_interval()]
 #'
 #' @family multiple set operations
 #' @seealso

R/bed_merge.r

@@ -1,16 +1,16 @@
 #' Merge overlapping intervals.
 #'
 #' Operations can be performed on merged intervals by specifying name-value
-#' pairs. Default \code{max_dist} of \code{0} means book-ended intervals are
+#' pairs. Default `max_dist` of `0` means book-ended intervals are
 #' merged.
 #'
-#' @param x \code{\link{tbl_interval}}
+#' @param x [tbl_interval()]
 #' @param max_dist maximum distance between intervals to merge
 #' @param ... name-value pairs that specify operations on merged intervals
 #'
 #' @template groups
 #'
-#' @return \code{\link{tbl_interval}}
+#' @return [tbl_interval()]
 #' @family single set operations
 #' @seealso
 #' \url{http://bedtools.readthedocs.org/en/latest/content/tools/merge.html}