Modify a Ranges object
# S3 method for Ranges
mutate(.data, ...)a Ranges object
Pairs of name-value expressions. The name-value pairs can either create new metadata columns or modify existing ones.
a Ranges object
df <- data.frame(start = 1:10,
width = 5,
seqnames = "seq1",
strand = sample(c("+", "-", "*"), 10, replace = TRUE),
gc = runif(10))
rng <- as_granges(df)
# mutate adds new columns
rng %>%
mutate(avg_gc = mean(gc), row_id = 1:n())
#> GRanges object with 10 ranges and 3 metadata columns:
#> seqnames ranges strand | gc avg_gc row_id
#> <Rle> <IRanges> <Rle> | <numeric> <numeric> <integer>
#> [1] seq1 1-5 - | 0.884227 0.340702 1
#> [2] seq1 2-6 * | 0.207714 0.340702 2
#> [3] seq1 3-7 - | 0.307086 0.340702 3
#> [4] seq1 4-8 + | 0.330530 0.340702 4
#> [5] seq1 5-9 * | 0.198679 0.340702 5
#> [6] seq1 6-10 * | 0.235694 0.340702 6
#> [7] seq1 7-11 + | 0.274887 0.340702 7
#> [8] seq1 8-12 * | 0.591321 0.340702 8
#> [9] seq1 9-13 - | 0.253391 0.340702 9
#> [10] seq1 10-14 - | 0.123487 0.340702 10
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# can also compute on newly created columns
rng %>%
mutate(score = gc * width, score2 = score + 1)
#> GRanges object with 10 ranges and 3 metadata columns:
#> seqnames ranges strand | gc score score2
#> <Rle> <IRanges> <Rle> | <numeric> <numeric> <numeric>
#> [1] seq1 1-5 - | 0.884227 4.421135 5.42114
#> [2] seq1 2-6 * | 0.207714 1.038569 2.03857
#> [3] seq1 3-7 - | 0.307086 1.535429 2.53543
#> [4] seq1 4-8 + | 0.330530 1.652649 2.65265
#> [5] seq1 5-9 * | 0.198679 0.993395 1.99340
#> [6] seq1 6-10 * | 0.235694 1.178472 2.17847
#> [7] seq1 7-11 + | 0.274887 1.374433 2.37443
#> [8] seq1 8-12 * | 0.591321 2.956605 3.95661
#> [9] seq1 9-13 - | 0.253391 1.266953 2.26695
#> [10] seq1 10-14 - | 0.123487 0.617436 1.61744
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# group by partitions the data and computes within each group
rng %>%
group_by(strand) %>%
mutate(avg_gc = mean(gc), row_id = 1:n())
#> GRanges object with 10 ranges and 3 metadata columns:
#> Groups: strand [3]
#> seqnames ranges strand | gc avg_gc row_id
#> <Rle> <IRanges> <Rle> | <numeric> <numeric> <integer>
#> [1] seq1 1-5 - | 0.884227 0.392048 1
#> [2] seq1 2-6 * | 0.207714 0.308352 1
#> [3] seq1 3-7 - | 0.307086 0.392048 2
#> [4] seq1 4-8 + | 0.330530 0.302708 1
#> [5] seq1 5-9 * | 0.198679 0.308352 2
#> [6] seq1 6-10 * | 0.235694 0.308352 3
#> [7] seq1 7-11 + | 0.274887 0.302708 2
#> [8] seq1 8-12 * | 0.591321 0.308352 4
#> [9] seq1 9-13 - | 0.253391 0.392048 3
#> [10] seq1 10-14 - | 0.123487 0.392048 4
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# mutate can be used in conjuction with anchoring to resize ranges
rng %>%
mutate(width = 10)
#> GRanges object with 10 ranges and 1 metadata column:
#> seqnames ranges strand | gc
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] seq1 1-10 - | 0.884227
#> [2] seq1 2-11 * | 0.207714
#> [3] seq1 3-12 - | 0.307086
#> [4] seq1 4-13 + | 0.330530
#> [5] seq1 5-14 * | 0.198679
#> [6] seq1 6-15 * | 0.235694
#> [7] seq1 7-16 + | 0.274887
#> [8] seq1 8-17 * | 0.591321
#> [9] seq1 9-18 - | 0.253391
#> [10] seq1 10-19 - | 0.123487
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# by default width modfication fixes by start
rng %>%
anchor_start() %>%
mutate(width = 10)
#> GRanges object with 10 ranges and 1 metadata column:
#> seqnames ranges strand | gc
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] seq1 1-10 - | 0.884227
#> [2] seq1 2-11 * | 0.207714
#> [3] seq1 3-12 - | 0.307086
#> [4] seq1 4-13 + | 0.330530
#> [5] seq1 5-14 * | 0.198679
#> [6] seq1 6-15 * | 0.235694
#> [7] seq1 7-16 + | 0.274887
#> [8] seq1 8-17 * | 0.591321
#> [9] seq1 9-18 - | 0.253391
#> [10] seq1 10-19 - | 0.123487
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# fix by end or midpoint
rng %>%
anchor_end() %>%
mutate(width = width + 1)
#> GRanges object with 10 ranges and 1 metadata column:
#> seqnames ranges strand | gc
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] seq1 0-5 - | 0.884227
#> [2] seq1 1-6 * | 0.207714
#> [3] seq1 2-7 - | 0.307086
#> [4] seq1 3-8 + | 0.330530
#> [5] seq1 4-9 * | 0.198679
#> [6] seq1 5-10 * | 0.235694
#> [7] seq1 6-11 + | 0.274887
#> [8] seq1 7-12 * | 0.591321
#> [9] seq1 8-13 - | 0.253391
#> [10] seq1 9-14 - | 0.123487
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
rng %>%
anchor_center() %>%
mutate(width = width + 1)
#> GRanges object with 10 ranges and 1 metadata column:
#> seqnames ranges strand | gc
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] seq1 0-5 - | 0.884227
#> [2] seq1 1-6 * | 0.207714
#> [3] seq1 2-7 - | 0.307086
#> [4] seq1 3-8 + | 0.330530
#> [5] seq1 4-9 * | 0.198679
#> [6] seq1 5-10 * | 0.235694
#> [7] seq1 6-11 + | 0.274887
#> [8] seq1 7-12 * | 0.591321
#> [9] seq1 8-13 - | 0.253391
#> [10] seq1 9-14 - | 0.123487
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# anchoring by strand
rng %>%
anchor_3p() %>%
mutate(width = width * 2)
#> GRanges object with 10 ranges and 1 metadata column:
#> seqnames ranges strand | gc
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] seq1 1-10 - | 0.884227
#> [2] seq1 -3-6 * | 0.207714
#> [3] seq1 3-12 - | 0.307086
#> [4] seq1 -1-8 + | 0.330530
#> [5] seq1 0-9 * | 0.198679
#> [6] seq1 1-10 * | 0.235694
#> [7] seq1 2-11 + | 0.274887
#> [8] seq1 3-12 * | 0.591321
#> [9] seq1 9-18 - | 0.253391
#> [10] seq1 10-19 - | 0.123487
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
rng %>%
anchor_5p() %>%
mutate(width = width * 2)
#> GRanges object with 10 ranges and 1 metadata column:
#> seqnames ranges strand | gc
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] seq1 -4-5 - | 0.884227
#> [2] seq1 2-11 * | 0.207714
#> [3] seq1 -2-7 - | 0.307086
#> [4] seq1 4-13 + | 0.330530
#> [5] seq1 5-14 * | 0.198679
#> [6] seq1 6-15 * | 0.235694
#> [7] seq1 7-16 + | 0.274887
#> [8] seq1 8-17 * | 0.591321
#> [9] seq1 4-13 - | 0.253391
#> [10] seq1 5-14 - | 0.123487
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths