Reduce then aggregate a Ranges object
reduce_ranges(.data, min.gapwidth = 1L, ...)
reduce_ranges_directed(.data, min.gapwidth = 1L, ...)a Ranges object to reduce
Ranges separated by a gap of at least min.gapwidth positions are not merged.
Name-value pairs of summary functions.
a Ranges object with the
set.seed(10)
df <- data.frame(start = sample(1:10),
width = 5,
seqnames = "seq1",
strand = sample(c("+", "-", "*"), 10, replace = TRUE),
gc = runif(10))
rng <- as_granges(df)
rng %>% reduce_ranges()
#> GRanges object with 1 range and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] seq1 1-14 *
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
rng %>% reduce_ranges(gc = mean(gc))
#> GRanges object with 1 range and 1 metadata column:
#> seqnames ranges strand | gc
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] seq1 1-14 * | 0.583196
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
rng %>% reduce_ranges_directed(gc = mean(gc))
#> GRanges object with 4 ranges and 1 metadata column:
#> seqnames ranges strand | gc
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] seq1 1-5 + | 0.500503
#> [2] seq1 9-13 + | 0.535597
#> [3] seq1 3-12 - | 0.558135
#> [4] seq1 2-14 * | 0.640830
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
rng %>% reduce_ranges_directed(gc = mean(gc), min.gapwidth = 10)
#> GRanges object with 3 ranges and 1 metadata column:
#> seqnames ranges strand | gc
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] seq1 1-13 + | 0.518050
#> [2] seq1 3-12 - | 0.558135
#> [3] seq1 2-14 * | 0.640830
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
x <- data.frame(start = c(11:13, 2, 7:6),
width=3,
id=sample(letters[1:3], 6, replace = TRUE),
score= sample(1:6))
x <- as_iranges(x)
x %>% reduce_ranges()
#> IRanges object with 3 ranges and 0 metadata columns:
#> start end width
#> <integer> <integer> <integer>
#> [1] 2 4 3
#> [2] 6 9 4
#> [3] 11 15 5
x %>% reduce_ranges(score = sum(score))
#> IRanges object with 3 ranges and 1 metadata column:
#> start end width | score
#> <integer> <integer> <integer> | <integer>
#> [1] 2 4 3 | 5
#> [2] 6 9 4 | 5
#> [3] 11 15 5 | 11
x %>% group_by(id) %>% reduce_ranges(score = sum(score))
#> IRanges object with 4 ranges and 2 metadata columns:
#> start end width | id score
#> <integer> <integer> <integer> | <character> <integer>
#> [1] 11 13 3 | c 2
#> [2] 2 4 3 | b 5
#> [3] 12 15 4 | b 9
#> [4] 6 9 4 | a 5