Package 'valr'

Description

Computes the absolute distance between the midpoint of each x interval and the midpoints of each closest y interval.

Usage

bed_absdist(x, y, genome)

Arguments

Details

Absolute distances are scaled by the inter-reference gap for the 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 x interval has no matching y chromosome, .absdist is NA.

$d_i(x,y) = min_k(|q_i - r_k|)\frac{R}{Length\ of\ chromosome}$

Both absolute and scaled distances are reported as .absdist and .absdist_scaled.

Interval statistics can be used in combination with dplyr::group_by() and dplyr::do() to calculate statistics for subsets of data. See vignette('interval-stats') for examples.

Value

ivl_df with .absdist and .absdist_scaled columns.

See Also

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002529

Other interval statistics: bed_fisher(), bed_jaccard(), bed_projection(), bed_reldist()

Examples

genome <- read_genome(valr_example("hg19.chrom.sizes.gz"))

x <- bed_random(genome, seed = 1010486)
y <- bed_random(genome, seed = 9203911)

bed_absdist(x, y, genome)

Description

Identify closest intervals.

Usage

bed_closest(x, y, overlap = TRUE, suffix = c(".x", ".y"))

Arguments

Details

input tbls are grouped by chrom by default, and additional groups can be added using dplyr::group_by(). For example, grouping by strand will constrain analyses to the same strand. To compare opposing strands across two tbls, strands on the y tbl can first be inverted using flip_strands().

Value

ivl_df with additional columns:

• .overlap amount of overlap with overlapping interval. Non-overlapping or adjacent intervals have an overlap of 0. .overlap will not be included in the output if overlap = FALSE.

• .dist distance to closest interval. Negative distances denote upstream intervals. Book-ended intervals have a distance of 1.

Note

For each interval in x bed_closest() returns overlapping intervals from y and the closest non-intersecting y interval. Setting overlap = FALSE will report the closest non-intersecting y intervals, ignoring any overlapping y intervals.

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/closest.html

Other multiple set operations: bed_coverage(), bed_intersect(), bed_map(), bed_subtract(), bed_window()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 100,    125
)

y <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 25,     50,
  "chr1", 140,    175
)

bed_glyph(bed_closest(x, y))

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 500,    600,
  "chr2", 5000,   6000
)

y <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 100,    200,
  "chr1", 150,    200,
  "chr1", 550,    580,
  "chr2", 7000,   8500
)

bed_closest(x, y)

bed_closest(x, y, overlap = FALSE)

# Report distance based on strand
x <- tibble::tribble(
  ~chrom, ~start, ~end, ~name, ~score, ~strand,
  "chr1", 10, 20, "a", 1, "-"
)

y <- tibble::tribble(
  ~chrom, ~start, ~end, ~name, ~score, ~strand,
  "chr1", 8, 9, "b", 1, "+",
  "chr1", 21, 22, "b", 1, "-"
)

res <- bed_closest(x, y)

# convert distance based on strand
res$.dist_strand <- ifelse(res$strand.x == "+", res$.dist, -(res$.dist))
res

# report absolute distances
res$.abs_dist <- abs(res$.dist)
res

Description

The output .id column can be used in downstream grouping operations. Default max_dist = 0 means that both overlapping and book-ended intervals will be clustered.

Usage

bed_cluster(x, max_dist = 0)

Arguments

Details

input tbls are grouped by chrom by default, and additional groups can be added using dplyr::group_by(). For example, grouping by strand will constrain analyses to the same strand. To compare opposing strands across two tbls, strands on the y tbl can first be inverted using flip_strands().

Value

ivl_df with .id column specifying sets of clustered intervals.

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/cluster.html

Other single set operations: bed_complement(), bed_flank(), bed_genomecov(), bed_merge(), bed_partition(), bed_shift(), bed_slop()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 100,    200,
  "chr1", 180,    250,
  "chr1", 250,    500,
  "chr1", 501,    1000,
  "chr2", 1,      100,
  "chr2", 150,    200
)

bed_cluster(x)

# glyph illustrating clustering of overlapping and book-ended intervals
x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 1,      10,
  "chr1", 5,      20,
  "chr1", 30,     40,
  "chr1", 40,     50,
  "chr1", 80,     90
)

bed_glyph(bed_cluster(x), label = ".id")

Description

Identify intervals in a genome not covered by a query.

Usage

bed_complement(x, genome)

Arguments

Value

ivl_df

See Also

Other single set operations: bed_cluster(), bed_flank(), bed_genomecov(), bed_merge(), bed_partition(), bed_shift(), bed_slop()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 0,      10,
  "chr1", 75,     100
)

genome <- tibble::tribble(
  ~chrom, ~size,
  "chr1", 200
)

bed_glyph(bed_complement(x, genome))

genome <- tibble::tribble(
  ~chrom,  ~size,
  "chr1",  500,
  "chr2",  600,
  "chr3",  800
)

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 100,    300,
  "chr1", 200,    400,
  "chr2", 0,      100,
  "chr2", 200,    400,
  "chr3", 500,    600
)

# intervals not covered by x
bed_complement(x, genome)

Description

Compute coverage of intervals.

Usage

bed_coverage(x, y, ...)

Arguments

Details

input tbls are grouped by chrom by default, and additional groups can be added using dplyr::group_by(). For example, grouping by strand will constrain analyses to the same strand. To compare opposing strands across two tbls, strands on the y tbl can first be inverted using flip_strands().

Value

ivl_df with the following additional columns:

• .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 the number of y intervals

Note

Book-ended intervals are included in coverage calculations.

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html

Other multiple set operations: bed_closest(), bed_intersect(), bed_map(), bed_subtract(), bed_window()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end, ~strand,
  "chr1", 100,    500,  "+",
  "chr2", 200,    400,  "+",
  "chr2", 300,    500,  "-",
  "chr2", 800,    900,  "-"
)

y <- tibble::tribble(
  ~chrom, ~start, ~end, ~value, ~strand,
  "chr1", 150,    400,  100,    "+",
  "chr1", 500,    550,  100,    "+",
  "chr2", 230,    430,  200,    "-",
  "chr2", 350,    430,  300,    "-"
)

bed_coverage(x, y)

Description

Calculate Fisher's test on number of intervals that are shared and unique between two sets of x and y intervals.

Usage

bed_fisher(x, y, genome)

Arguments

Details

Interval statistics can be used in combination with dplyr::group_by() and dplyr::do() to calculate statistics for subsets of data. See vignette('interval-stats') for examples.

Value

ivl_df

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/fisher.html

Other interval statistics: bed_absdist(), bed_jaccard(), bed_projection(), bed_reldist()

Examples

genome <- read_genome(valr_example("hg19.chrom.sizes.gz"))

x <- bed_random(genome, n = 1e4, seed = 1010486)
y <- bed_random(genome, n = 1e4, seed = 9203911)

bed_fisher(x, y, genome)

Description

Create flanking intervals from input intervals.

Usage

bed_flank(
  x,
  genome,
  both = 0,
  left = 0,
  right = 0,
  fraction = FALSE,
  strand = FALSE,
  trim = FALSE,
  ...
)

Arguments

Value

ivl_df

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/flank.html

Other single set operations: bed_cluster(), bed_complement(), bed_genomecov(), bed_merge(), bed_partition(), bed_shift(), bed_slop()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 25, 50,
  "chr1", 100, 125
)

genome <- tibble::tribble(
  ~chrom, ~size,
  "chr1", 130
)

bed_glyph(bed_flank(x, genome, both = 20))

x <- tibble::tribble(
  ~chrom, ~start, ~end, ~name, ~score, ~strand,
  "chr1", 500,    1000, ".",   ".",    "+",
  "chr1", 1000,   1500, ".",   ".",    "-"
)

genome <- tibble::tribble(
  ~chrom, ~size,
  "chr1", 5000
)

bed_flank(x, genome, left = 100)

bed_flank(x, genome, right = 100)

bed_flank(x, genome, both = 100)

bed_flank(x, genome, both = 0.5, fraction = TRUE)

Description

This function is useful for calculating interval coverage across an entire genome.

Usage

bed_genomecov(x, genome, zero_depth = FALSE)

Arguments

Details

input tbls are grouped by chrom by default, and additional groups can be added using dplyr::group_by(). For example, grouping by strand will constrain analyses to the same strand. To compare opposing strands across two tbls, strands on the y tbl can first be inverted using flip_strands().

Value

ivl_df with the an additional column:

• .depth depth of interval coverage

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html

Other single set operations: bed_cluster(), bed_complement(), bed_flank(), bed_merge(), bed_partition(), bed_shift(), bed_slop()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end, ~strand,
  "chr1", 20, 70, "+",
  "chr1", 50, 100, "-",
  "chr1", 200, 250, "+",
  "chr1", 220, 250, "+"
)

genome <- tibble::tribble(
  ~chrom, ~size,
  "chr1", 500,
  "chr2", 1000
)

bed_genomecov(x, genome)

bed_genomecov(dplyr::group_by(x, strand), genome)

bed_genomecov(dplyr::group_by(x, strand), genome, zero_depth = TRUE)

Description

Used to illustrate the output of valr functions with small examples.

Usage

bed_glyph(expr, label = NULL)

Arguments

Value

ggplot2::ggplot()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 25,     50,
  "chr1", 100,    125
)

y <- tibble::tribble(
  ~chrom, ~start, ~end, ~value,
  "chr1", 30, 75, 50
)

bed_glyph(bed_intersect(x, y))

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 30,     75,
  "chr1", 50,     90,
  "chr1", 91,     120
)

bed_glyph(bed_merge(x))

bed_glyph(bed_cluster(x), label = ".id")

Description

Report intersecting intervals from x and y tbls. Book-ended intervals have .overlap values of 0 in the output.

Usage

bed_intersect(x, ..., invert = FALSE, suffix = c(".x", ".y"))

Arguments

Details

input tbls are grouped by chrom by default, and additional groups can be added using dplyr::group_by(). For example, grouping by strand will constrain analyses to the same strand. To compare opposing strands across two tbls, strands on the y tbl can first be inverted using flip_strands().

Value

ivl_df 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 y tbls are supplied, the .source contains variable names associated with each interval. All original columns from the y are suffixed with .y in the output.

If ... contains named inputs (i.e ⁠a = y, b = z⁠ or list(a = y, b = z)), then .source will contain supplied names (see examples).

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html

Other multiple set operations: bed_closest(), bed_coverage(), bed_map(), bed_subtract(), bed_window()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 25, 50,
  "chr1", 100, 125
)

y <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 30,     75
)

bed_glyph(bed_intersect(x, y))

bed_glyph(bed_intersect(x, y, invert = TRUE))

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 100,    500,
  "chr2", 200,    400,
  "chr2", 300,    500,
  "chr2", 800,    900
)

y <- tibble::tribble(
  ~chrom, ~start, ~end, ~value,
  "chr1", 150,    400,  100,
  "chr1", 500,    550,  100,
  "chr2", 230,    430,  200,
  "chr2", 350,    430,  300
)

bed_intersect(x, y)

bed_intersect(x, y, invert = TRUE)

# start and end of each overlapping interval
res <- bed_intersect(x, y)
dplyr::mutate(res,
  start = pmax(start.x, start.y),
  end = pmin(end.x, end.y)
)

z <- tibble::tribble(
  ~chrom, ~start, ~end, ~value,
  "chr1", 150,    400,  100,
  "chr1", 500,    550,  100,
  "chr2", 230,    430,  200,
  "chr2", 750,    900,  400
)

bed_intersect(x, y, z)

bed_intersect(x, exons = y, introns = z)

# a list of tbl_intervals can also be passed
bed_intersect(x, list(exons = y, introns = z))

Description

Quantifies the extent of overlap between to sets of intervals in terms of base-pairs. Groups that are shared between input are used to calculate the statistic for subsets of data.

Usage

bed_jaccard(x, y)

Arguments

Details

The Jaccard statistic takes values of ⁠[0,1]⁠ and is measured as:

$J(x,y) = \frac{\mid x \bigcap y \mid} {\mid x \bigcup y \mid} = \frac{\mid x \bigcap y \mid} {\mid x \mid + \mid y \mid - \mid x \bigcap y \mid}$

Interval statistics can be used in combination with dplyr::group_by() and dplyr::do() to calculate statistics for subsets of data. See vignette('interval-stats') for examples.

Value

tibble with the following columns:

• len_i length of the intersection in base-pairs

• len_u length of the union in base-pairs

• jaccard value of jaccard statistic

• n_int number of intersecting intervals between x and y

If inputs are grouped, the return value will contain one set of values per group.

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/jaccard.html

Other interval statistics: bed_absdist(), bed_fisher(), bed_projection(), bed_reldist()

Examples

genome <- read_genome(valr_example("hg19.chrom.sizes.gz"))

x <- bed_random(genome, seed = 1010486)
y <- bed_random(genome, seed = 9203911)

bed_jaccard(x, y)

# calculate jaccard per chromosome
bed_jaccard(
  dplyr::group_by(x, chrom),
  dplyr::group_by(y, chrom)
)

Description

Divide intervals into new sub-intervals ("windows").

Usage

bed_makewindows(x, win_size = 0, step_size = 0, num_win = 0, reverse = FALSE)

Arguments

Value

ivl_df with .win_id column that contains a numeric identifier for the window.

Note

The name and .win_id columns can be used to create new interval names (see 'namenum' example below) or in subsequent group_by operations (see vignette).

See Also

Other utilities: bed12_to_exons(), bound_intervals(), flip_strands(), interval_spacing()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end, ~name, ~score, ~strand,
  "chr1", 100,    200,  "A",   ".",    "+"
)

bed_glyph(bed_makewindows(x, num_win = 10), label = ".win_id")

# Fixed number of windows
bed_makewindows(x, num_win = 10)

# Fixed window size
bed_makewindows(x, win_size = 10)

# Fixed window size with overlaps
bed_makewindows(x, win_size = 10, step_size = 5)

# reverse win_id
bed_makewindows(x, win_size = 10, reverse = TRUE)

# bedtools 'namenum'
wins <- bed_makewindows(x, win_size = 10)
dplyr::mutate(wins, namenum = stringr::str_c(name, "_", .win_id))

Description

Apply functions like min() and max() to intersecting intervals. bed_map() uses bed_intersect() to identify intersecting intervals, so output columns will be suffixed with .x and .y. Expressions that refer to input columns from x and y columns must take these suffixes into account.

Usage

bed_map(x, y, ..., min_overlap = 1)

concat(.data, sep = ",")

values_unique(.data, sep = ",")

values(.data, sep = ",")

Arguments

Details

Book-ended intervals can be included by setting min_overlap = 0.

Non-intersecting intervals from x are included in the result with NA values.

input tbls are grouped by chrom by default, and additional groups can be added using dplyr::group_by(). For example, grouping by strand will constrain analyses to the same strand. To compare opposing strands across two tbls, strands on the y tbl can first be inverted using flip_strands().

Value

ivl_df

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/map.html

Other multiple set operations: bed_closest(), bed_coverage(), bed_intersect(), bed_subtract(), bed_window()

Examples

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))

Description

Operations can be performed on merged intervals by specifying name-value pairs. Default max_dist of 0 means book-ended intervals are merged.

Usage

bed_merge(x, max_dist = 0, ...)

Arguments

Details

input tbls are grouped by chrom by default, and additional groups can be added using dplyr::group_by(). For example, grouping by strand will constrain analyses to the same strand. To compare opposing strands across two tbls, strands on the y tbl can first be inverted using flip_strands().

Value

ivl_df

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/merge.html

Other single set operations: bed_cluster(), bed_complement(), bed_flank(), bed_genomecov(), bed_partition(), bed_shift(), bed_slop()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 1, 50,
  "chr1", 10, 75,
  "chr1", 100, 120
)

bed_glyph(bed_merge(x))

x <- tibble::tribble(
  ~chrom, ~start, ~end, ~value, ~strand,
  "chr1", 1,      50,   1,      "+",
  "chr1", 100,    200,  2,      "+",
  "chr1", 150,    250,  3,      "-",
  "chr2", 1,      25,   4,      "+",
  "chr2", 200,    400,  5,      "-",
  "chr2", 400,    500,  6,      "+",
  "chr2", 450,    550,  7,      "+"
)

bed_merge(x)

bed_merge(x, max_dist = 100)

# merge intervals on same strand
bed_merge(dplyr::group_by(x, strand))

bed_merge(x, .value = sum(value))

Description

Convert a set of intervals into elemental intervals that contain each start and end position in the set.

Usage

bed_partition(x, ...)

Arguments

Details

Summary operations, such as min() or max() can be performed on elemental intervals by specifying name-value pairs.

This function is useful for calculating summaries across overlapping intervals without merging the intervals.

input tbls are grouped by chrom by default, and additional groups can be added using dplyr::group_by(). For example, grouping by strand will constrain analyses to the same strand. To compare opposing strands across two tbls, strands on the y tbl can first be inverted using flip_strands().

Value

ivl_df()

See Also

https://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedops.html#partition-p-partition

Other single set operations: bed_cluster(), bed_complement(), bed_flank(), bed_genomecov(), bed_merge(), bed_shift(), bed_slop()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end, ~value, ~strand,
  "chr1", 100, 500, 10, "+",
  "chr1", 200, 400, 20, "-",
  "chr1", 300, 550, 30, "+",
  "chr1", 550, 575, 2, "+",
  "chr1", 800, 900, 5, "+"
)


bed_glyph(bed_partition(x))
bed_glyph(bed_partition(x, value = sum(value)), label = "value")

bed_partition(x)

# compute summary over each elemental interval
bed_partition(x, value = sum(value))

# partition and compute summaries based on group
x <- dplyr::group_by(x, strand)
bed_partition(x, value = sum(value))

# combine values across multiple tibbles
y <- tibble::tribble(
  ~chrom, ~start, ~end, ~value, ~strand,
  "chr1", 10, 500, 100, "+",
  "chr1", 250, 420, 200, "-",
  "chr1", 350, 550, 300, "+",
  "chr1", 550, 555, 20, "+",
  "chr1", 800, 900, 50, "+"
)

x <- dplyr::bind_rows(x, y)
bed_partition(x, value = sum(value))

Description

Projection test for query interval overlap.

Usage

bed_projection(x, y, genome, by_chrom = FALSE)

Arguments

Details

Interval statistics can be used in combination with dplyr::group_by() and dplyr::do() to calculate statistics for subsets of data. See vignette('interval-stats') for examples.

Value

ivl_df with the following columns:

• chrom the name of chromosome tested if by_chrom = TRUE, otherwise has a value of whole_genome

• p.value p-value from a binomial test. p-values > 0.5 are converted to 1 - p-value and lower_tail is FALSE

• obs_exp_ratio ratio of observed to expected overlap frequency

• lower_tail TRUE indicates the observed overlaps are in the lower tail of the distribution (e.g., less overlap than expected). FALSE indicates that the observed overlaps are in the upper tail of the distribution (e.g., more overlap than expected)

See Also

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002529

Other interval statistics: bed_absdist(), bed_fisher(), bed_jaccard(), bed_reldist()

Examples

genome <- read_genome(valr_example("hg19.chrom.sizes.gz"))

x <- bed_random(genome, seed = 1010486)
y <- bed_random(genome, seed = 9203911)

bed_projection(x, y, genome)

bed_projection(x, y, genome, by_chrom = TRUE)

Description

Generate randomly placed intervals on a genome.

Usage

bed_random(genome, length = 1000, n = 1e+06, seed = 0, sorted = TRUE)

Arguments

Details

Sorting can be suppressed with sorted = FALSE.

Value

ivl_df

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/random.html

Other randomizing operations: bed_shuffle()

Examples

genome <- tibble::tribble(
  ~chrom,  ~size,
  "chr1",  10000000,
  "chr2",  50000000,
  "chr3",  60000000,
  "chrX",  5000000
)

bed_random(genome, seed = 10104)

# sorting can be suppressed
bed_random(genome, sorted = FALSE, seed = 10104)

# 500 random intervals of length 500
bed_random(genome, length = 500, n = 500, seed = 10104)

Description

Compute relative distances between intervals.

Usage

bed_reldist(x, y, detail = FALSE)

Arguments

Details

Interval statistics can be used in combination with dplyr::group_by() and dplyr::do() to calculate statistics for subsets of data. See vignette('interval-stats') for examples.

Value

If detail = FALSE, a ivl_df that summarizes calculated .reldist values with the following columns:

• .reldist relative distance metric

• .counts number of metric observations

• .total total observations

• .freq frequency of observation

If detail = TRUE, the .reldist column reports the relative distance for each input x interval.

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/reldist.html

Other interval statistics: bed_absdist(), bed_fisher(), bed_jaccard(), bed_projection()

Examples

genome <- read_genome(valr_example("hg19.chrom.sizes.gz"))

x <- bed_random(genome, seed = 1010486)
y <- bed_random(genome, seed = 9203911)

bed_reldist(x, y)

bed_reldist(x, y, detail = TRUE)

Description

Out-of-bounds intervals are removed by default.

Usage

bed_shift(x, genome, size = 0, fraction = 0, trim = FALSE)

Arguments

Value

ivl_df

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/shift.html

Other single set operations: bed_cluster(), bed_complement(), bed_flank(), bed_genomecov(), bed_merge(), bed_partition(), bed_slop()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 25, 50,
  "chr1", 100, 125
)

genome <- tibble::tribble(
  ~chrom, ~size,
  "chr1", 125
)

bed_glyph(bed_shift(x, genome, size = -20))

x <- tibble::tribble(
  ~chrom, ~start, ~end, ~strand,
  "chr1", 100,    150,  "+",
  "chr1", 200,    250,  "+",
  "chr2", 300,    350,  "+",
  "chr2", 400,    450,  "-",
  "chr3", 500,    550,  "-",
  "chr3", 600,    650,  "-"
)

genome <- tibble::tribble(
  ~chrom, ~size,
  "chr1", 1000,
  "chr2", 2000,
  "chr3", 3000
)

bed_shift(x, genome, 100)

bed_shift(x, genome, fraction = 0.5)

# shift with respect to strand
stranded <- dplyr::group_by(x, strand)
bed_shift(stranded, genome, 100)

Description

Shuffle input intervals.

Usage

bed_shuffle(
  x,
  genome,
  incl = NULL,
  excl = NULL,
  max_tries = 1000,
  within = FALSE,
  seed = 0
)

Arguments

Value

ivl_df

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/shuffle.html

Other randomizing operations: bed_random()

Examples

genome <- tibble::tribble(
  ~chrom, ~size,
  "chr1", 1e6,
  "chr2", 2e6,
  "chr3", 4e6
)

x <- bed_random(genome, seed = 1010486)

bed_shuffle(x, genome, seed = 9830491)

Description

Increase the size of input intervals.

Usage

bed_slop(
  x,
  genome,
  both = 0,
  left = 0,
  right = 0,
  fraction = FALSE,
  strand = FALSE,
  trim = FALSE,
  ...
)

Arguments

Value

ivl_df

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/slop.html

Other single set operations: bed_cluster(), bed_complement(), bed_flank(), bed_genomecov(), bed_merge(), bed_partition(), bed_shift()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 110,    120,
  "chr1", 225,    235
)

genome <- tibble::tribble(
  ~chrom, ~size,
  "chr1", 400
)

bed_glyph(bed_slop(x, genome, both = 20, trim = TRUE))

genome <- tibble::tribble(
  ~chrom, ~size,
  "chr1", 5000
)

x <- tibble::tribble(
  ~chrom, ~start, ~end, ~name, ~score, ~strand,
  "chr1", 500, 1000, ".", ".", "+",
  "chr1", 1000, 1500, ".", ".", "-"
)

bed_slop(x, genome, left = 100)

bed_slop(x, genome, right = 100)

bed_slop(x, genome, both = 100)

bed_slop(x, genome, both = 0.5, fraction = TRUE)

Description

Sort a set of intervals.

Usage

bed_sort(x, by_size = FALSE, by_chrom = FALSE, reverse = FALSE)

Arguments

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/sort.html

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr8", 500,    1000,
  "chr8", 1000,   5000,
  "chr8", 100,    200,
  "chr1", 100,    300,
  "chr1", 100,    200
)

# sort by chrom and start
bed_sort(x)

# reverse sort order
bed_sort(x, reverse = TRUE)

# sort by interval size
bed_sort(x, by_size = TRUE)

# sort by decreasing interval size
bed_sort(x, by_size = TRUE, reverse = TRUE)

# sort by interval size within chrom
bed_sort(x, by_size = TRUE, by_chrom = TRUE)

Description

Subtract y intervals from x intervals.

Usage

bed_subtract(x, y, any = FALSE)

Arguments

Details

input tbls are grouped by chrom by default, and additional groups can be added using dplyr::group_by(). For example, grouping by strand will constrain analyses to the same strand. To compare opposing strands across two tbls, strands on the y tbl can first be inverted using flip_strands().

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html

Other multiple set operations: bed_closest(), bed_coverage(), bed_intersect(), bed_map(), bed_window()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 1,      100
)

y <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 50,     75
)

bed_glyph(bed_subtract(x, y))

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 100,    200,
  "chr1", 250,    400,
  "chr1", 500,    600,
  "chr1", 1000,   1200,
  "chr1", 1300,   1500
)

y <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 150,    175,
  "chr1", 510,    525,
  "chr1", 550,    575,
  "chr1", 900,    1050,
  "chr1", 1150,   1250,
  "chr1", 1299,   1501
)

bed_subtract(x, y)

bed_subtract(x, y, any = TRUE)

Description

Identify intervals within a specified distance.

Usage

bed_window(x, y, genome, ...)

Arguments

Details

input tbls are grouped by chrom by default, and additional groups can be added using dplyr::group_by(). For example, grouping by strand will constrain analyses to the same strand. To compare opposing strands across two tbls, strands on the y tbl can first be inverted using flip_strands().

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/window.html

Other multiple set operations: bed_closest(), bed_coverage(), bed_intersect(), bed_map(), bed_subtract()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 25,     50,
  "chr1", 100,    125
)

y <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 60,     75
)

genome <- tibble::tribble(
  ~chrom, ~size,
  "chr1", 125
)

bed_glyph(bed_window(x, y, genome, both = 15))

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 10, 100,
  "chr2", 200, 400,
  "chr2", 300, 500,
  "chr2", 800, 900
)

y <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 150,    400,
  "chr2", 230,    430,
  "chr2", 350,    430
)

genome <- tibble::tribble(
  ~chrom, ~size,
  "chr1", 500,
  "chr2", 1000
)

bed_window(x, y, genome, both = 100)

Description

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).

Usage

bed12_to_exons(x)

Arguments

See Also

Other utilities: bed_makewindows(), bound_intervals(), flip_strands(), interval_spacing()

Examples

x <- read_bed12(valr_example("mm9.refGene.bed.gz"))

bed12_to_exons(x)

Description

Used to remove out-of-bounds intervals, or trim interval coordinates using a genome.

Usage

bound_intervals(x, genome, trim = FALSE)

Arguments

Value

ivl_df

See Also

Other utilities: bed12_to_exons(), bed_makewindows(), flip_strands(), interval_spacing()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", -100,   500,
  "chr1", 100,    1e9,
  "chr1", 500,    1000
)

genome <- read_genome(valr_example("hg19.chrom.sizes.gz"))

# out-of-bounds are removed by default ...
bound_intervals(x, genome)

# ... or can be trimmed within the bounds of a genome
bound_intervals(x, genome, trim = TRUE)

Description

Numbers in the score column are intron numbers from 5' to 3' independent of strand. I.e., the first introns for + and - strand genes both have score values of 1.

Usage

create_introns(x)

Arguments

See Also

Other feature functions: create_tss(), create_utrs3(), create_utrs5()

Examples

x <- read_bed12(valr_example("mm9.refGene.bed.gz"))

create_introns(x)

Description

Create transcription start site features.

Usage

create_tss(x)

Arguments

See Also

Other feature functions: create_introns(), create_utrs3(), create_utrs5()

Examples

x <- read_bed12(valr_example("mm9.refGene.bed.gz"))

create_tss(x)

Description

Create 3' UTR features.

Usage

create_utrs3(x)

Arguments

See Also

Other feature functions: create_introns(), create_tss(), create_utrs5()

Examples

x <- read_bed12(valr_example("mm9.refGene.bed.gz"))

create_utrs3(x)

Description

Create 5' UTR features.

Usage

create_utrs5(x)

Arguments

See Also

Other feature functions: create_introns(), create_tss(), create_utrs3()

Examples

x <- read_bed12(valr_example("mm9.refGene.bed.gz"))

create_utrs5(x)

Description

Currently db_ucsc and db_ensembl are available for connections.

Usage

db_ucsc(
  dbname,
  host = "genome-mysql.cse.ucsc.edu",
  user = "genomep",
  password = "password",
  port = 3306,
  ...
)

db_ensembl(
  dbname,
  host = "ensembldb.ensembl.org",
  user = "anonymous",
  password = "",
  port = 3306,
  ...
)

Arguments

See Also

https://genome.ucsc.edu/goldenpath/help/mysql.html

https://www.ensembl.org/info/data/mysql.html

Examples

## Not run: 
if (require(RMariaDB)) {
  library(dplyr)
  ucsc <- db_ucsc("hg38")

  # fetch the `refGene` tbl
  tbl(ucsc, "refGene")

  # the `chromInfo` tbls have size information
  tbl(ucsc, "chromInfo")
}

## End(Not run)
## Not run: 
if (require(RMariaDB)) {
  library(dplyr)
  # squirrel genome
  ensembl <- db_ensembl("spermophilus_tridecemlineatus_core_67_2")

  tbl(ensembl, "gene")
}

## End(Not run)

Description

Flips positive (+) stranded intervals to negative (-) strands, and vice-versa. Facilitates comparisons among intervals on opposing strands.

Usage

flip_strands(x)

Arguments

See Also

Other utilities: bed12_to_exons(), bed_makewindows(), bound_intervals(), interval_spacing()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end, ~strand,
  "chr1", 1,      100,  "+",
  "chr2", 1,      100,  "-"
)

flip_strands(x)

Description

Convert Granges to bed tibble

Usage

gr_to_bed(x)

Arguments

Value

tibble::tibble()

Examples

## Not run: 
gr <- GenomicRanges::GRanges(
  seqnames = S4Vectors::Rle(
    c("chr1", "chr2", "chr1", "chr3"),
    c(1, 1, 1, 1)
  ),
  ranges = IRanges::IRanges(
    start = c(1, 10, 50, 100),
    end = c(100, 500, 1000, 2000),
    names = head(letters, 4)
  ),
  strand = S4Vectors::Rle(
    c("-", "+"), c(2, 2)
  )
)

gr_to_bed(gr)

# There are two ways to convert a bed-like data.frame to GRanges:

gr <- GenomicRanges::GRanges(
  seqnames = S4Vectors::Rle(x$chrom),
  ranges = IRanges::IRanges(
    start = x$start + 1,
    end = x$end,
    names = x$name
  ),
  strand = S4Vectors::Rle(x$strand)
)
# or:

gr <- GenomicRanges::makeGRangesFromDataFrame(dplyr::mutate(x, start = start + 1))

## End(Not run)

Description

Spacing for the first interval of each chromosome is undefined (NA). The leading interval of an overlapping interval pair has a negative value.

Usage

interval_spacing(x)

Arguments

Value

ivl_df with .spacing column.

See Also

Other utilities: bed12_to_exons(), bed_makewindows(), bound_intervals(), flip_strands()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 1,      100,
  "chr1", 150,    200,
  "chr2", 200,    300
)

interval_spacing(x)

Description

Required column names for interval dataframes are chrom, start and end. Internally interval dataframes are validated using check_interval()

Required column names for genome dataframes are chrom and size. Internally genome dataframes are validated using check_genome().

Usage

check_interval(x)

check_genome(x)

Arguments

Examples

# using tibble
x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 1, 50,
  "chr1", 10, 75,
  "chr1", 100, 120
)

check_interval(x)

# using base R data.frame
x <- data.frame(
  chrom = "chr1",
  start = 0,
  end = 100,
  stringsAsFactors = FALSE
)

check_interval(x)

# example genome input

x <- tibble::tribble(
  ~chrom, ~size,
  "chr1", 1e6
)

check_genome(x)

Description

read functions for BED and related formats. Filenames can be local file or URLs. The read functions load data into tbls with consistent chrom, start and end colnames.

Usage

read_bed(
  filename,
  col_types = bed12_coltypes,
  sort = TRUE,
  ...,
  n_fields = NULL
)

read_bed12(filename, ...)

read_bedgraph(filename, ...)

read_narrowpeak(filename, ...)

read_broadpeak(filename, ...)

Arguments

Details

https://genome.ucsc.edu/FAQ/FAQformat.html#format1

https://genome.ucsc.edu/FAQ/FAQformat.html#format1

https://genome.ucsc.edu/goldenPath/help/bedgraph.html

https://genome.ucsc.edu/FAQ/FAQformat.html#format12

https://genome.ucsc.edu/FAQ/FAQformat.html#format13

Value

ivl_df

See Also

Other read functions: read_genome(), read_vcf()

Examples

# read_bed assumes 3 field BED format.
read_bed(valr_example("3fields.bed.gz"))

# result is sorted by chrom and start unless `sort = FALSE`
read_bed(valr_example("3fields.bed.gz"), sort = FALSE)


read_bed12(valr_example("mm9.refGene.bed.gz"))


read_bedgraph(valr_example("test.bg.gz"))


read_narrowpeak(valr_example("sample.narrowPeak.gz"))


read_broadpeak(valr_example("sample.broadPeak.gz"))

Description

This function will output a 5 column tibble with zero-based chrom, start, end, score, and strand columns.

Usage

read_bigwig(path, set_strand = "+")

Arguments

Note

This functions uses rtracklayer to import bigwigs which has unstable support for the windows platform and therefore may error for windows users (particularly for 32 bit window users).

Examples

## Not run: 
if (.Platform$OS.type != "windows") {
  bw <- read_bigwig(valr_example("hg19.dnase1.bw"))
  head(bw)
}

## End(Not run)

Description

Genome files (UCSC "chromSize" files) contain chromosome name and size information. These sizes are used by downstream functions to identify computed intervals that have coordinates outside of the genome bounds.

Usage

read_genome(path)

Arguments

Value

genome_df, sorted by size

Note

URLs to genome files can also be used.

See Also

Other read functions: read_bed(), read_vcf()

Examples

read_genome(valr_example("hg19.chrom.sizes.gz"))

## Not run: 
# `read_genome` accepts a URL
read_genome("https://genome.ucsc.edu/goldenpath/help/hg19.chrom.sizes")

## End(Not run)

Description

This function will output a tibble with the required chrom, start, and end columns, as well as other columns depending on content in GTF/GFF file.

Usage

read_gtf(path, zero_based = TRUE)

Arguments

Examples

gtf <- read_gtf(valr_example("hg19.gencode.gtf.gz"))
head(gtf)

Description

Read a VCF file.

Usage

read_vcf(vcf)

Arguments

Value

data_frame

Note

return value has chrom, start and end columns. Interval lengths are the size of the 'REF' field.

See Also

Other read functions: read_bed(), read_genome()

Examples

vcf_file <- valr_example("test.vcf.gz")
read_vcf(vcf_file)

Description

valr provides tools to read and manipulate intervals and signals on a genome reference. valr was developed to facilitate interactive analysis of genome-scale data sets, leveraging the power of dplyr and piping.

Details

To learn more about valr, start with the vignette: browseVignettes(package = "valr")

Author(s)

Jay Hesselberth [email protected]

Kent Riemondy [email protected]

See Also

Report bugs at https://github.com/rnabioco/valr/issues

Description

Provide working directory for valr example files.

Usage

valr_example(path)

Arguments

Examples

valr_example("hg19.chrom.sizes.gz")