inst/example/bed_map.r

In rnabioco/valr: Genome Interval Arithmetic

x <- tibble::tribble(
  ~chrom,
  ~start,
  ~end,
  'chr1',
  100,
  250,
  'chr2',
  250,
  500
)

y <- tibble::tribble(
  ~chrom,
  ~start,
  ~end,
  ~value,
  'chr1',
  100,
  250,
  10,
  'chr1',
  150,
  250,
  20,
  'chr2',
  250,
  500,
  500
)

bed_glyph(bed_map(x, y, value = sum(value)), label = 'value')

# summary examples
bed_map(x, y, .sum = sum(value))

bed_map(x, y, .min = min(value), .max = max(value))

# identify non-intersecting intervals to include in the result
res <- bed_map(x, y, .sum = sum(value))
x_not <- bed_intersect(x, y, invert = TRUE)
dplyr::bind_rows(res, x_not)

# create a list-column
bed_map(x, y, .values = list(value))

# use `nth` family from dplyr
bed_map(x, y, .first = dplyr::first(value))

bed_map(x, y, .absmax = abs(max(value)))

bed_map(x, y, .count = length(value))

bed_map(x, y, .vals = values(value))

# count defaults are NA not 0; differs from bedtools2 ...
bed_map(x, y, .counts = dplyr::n())

# ... but NA counts can be coverted to 0's
dplyr::mutate(
  bed_map(x, y, .counts = dplyr::n()),
  .counts = ifelse(is.na(.counts), 0, .counts)
)