valr: Genome Interval Arithmetic in R
Version 0.2.0

Read and manipulate genome intervals and signals. Provides functionality similar to command-line tool suites within R, enabling interactive analysis and visualization of genome-scale data.

AuthorJay Hesselberth [aut, cre], Kent Riemondy [aut], Ryan Sheridan [ctb]
Date of publication2017-05-05 17:40:09 UTC
MaintainerJay Hesselberth <jay.hesselberth@gmail.com>
LicenseMIT + file LICENSE
Version0.2.0
URL http://github.com/rnabioco/valr/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("valr")

Getting started

README.md
Interval statistics
valr overview

Popular man pages

bed_cluster: Cluster neighboring intervals.
bed_flank: Create flanking intervals from input intervals.
bed_glyph: Create example glyphs for valr functions.
bed_merge: Merge overlapping intervals.
bed_reldist: Compute relative distances between intervals.
bed_slop: Increase the size of input intervals.
interval_spacing: Calculate interval spacing.
See all...

All man pages Function index File listing

Man pages

bed12_to_exons: Convert BED12 to individual exons in BED6.
bed_absdist: Compute absolute distances between intervals.
bed_closest: Identify closest intervals.
bed_cluster: Cluster neighboring intervals.
bed_complement: Identify intervals in a genome not covered by a query.
bed_coverage: Compute coverage of intervals.
bed_fisher: Fisher's test on number of shared and unique intervals.
bed_flank: Create flanking intervals from input intervals.
bed_glyph: Create example glyphs for valr functions.
bed_intersect: Identify intersecting intervals.
bed_jaccard: Calculate jaccard statistics on two sets of intervals.
bed_makewindows: Divide intervals into new sub-intervals ("windows").
bed_map: Calculate summaries and statistics from overlapping...
bed_merge: Merge overlapping intervals.
bed_projection: Projection test for query interval overlap.
bed_random: Generate randomly placed intervals on a genome.
bed_reldist: Compute relative distances between intervals.
bed_shift: Adjust intervals by a fixed size.
bed_shuffle: Shuffle input intervals.
bed_slop: Increase the size of input intervals.
bed_sort: Sort a tbl of intervals.
bed_subtract: Subtract intervals.
bed_window: Identify intervals within a specified distance.
bound_intervals: Select intervals bounded by a genome.
db: Fetch data from remote databases.
flip_strands: Flip strands in intervals.
interval_spacing: Calculate interval spacing.
is.tbl_genome: Test if the object is a tbl_genome.
is.tbl_interval: Test if the object is a tbl_interval.
read_bed: Read BED and related files.
read_genome: Read genome files.
read_vcf: Read a VCF file.
sorting: Sorting tbls of intervals
tbl_genome: Tibble for reference sizes.
tbl_interval: Tibble for intervals.
trbl_genome: Construct a tbl_genome using tribble formatting.
trbl_interval: Construct an tbl_interval using tribble formatting.
valr: valr: genome interval arithmetic in R
valr_example: Provide working directory for valr example files.

Functions

absdist_impl Source code
bed12_to_exons Man page Source code
bed_absdist Man page Source code
bed_closest Man page Source code
bed_cluster Man page Source code
bed_complement Man page Source code
bed_coverage Man page Source code
bed_fisher Man page Source code
bed_flank Man page Source code
bed_glyph Man page Source code
bed_intersect Man page Source code
bed_jaccard Man page Source code
bed_makewindows Man page Source code
bed_map Man page Source code
bed_merge Man page Source code
bed_projection Man page Source code
bed_random Man page Source code
bed_reldist Man page Source code
bed_shift Man page Source code
bed_shuffle Man page Source code
bed_slop Man page Source code
bed_sort Man page Source code
bed_subtract Man page Source code
bed_window Man page Source code
bound_intervals Man page Source code
check_genome Source code
check_interval Source code
check_names Source code
check_suffix Source code
closest_impl Source code
complement_impl Source code
concat Man page Source code
coverage_impl Source code
db Man page
db_ensembl Man page Source code
db_ucsc Man page Source code
flip_strands Man page Source code
get_labels Source code
glyph_plot Source code
glyph_theme Source code
intersect_impl Source code
interval_spacing Man page Source code
interval_union Source code
is.tbl_genome Man page Source code
is.tbl_interval Man page Source code
is_merged Source code
merge_impl Source code
random_impl Source code
read_bed Man page Source code
read_bed12 Man page Source code
read_bedgraph Man page Source code
read_broadpeak Man page Source code
read_genome Man page Source code
read_narrowpeak Man page Source code
read_vcf Man page Source code
reldist_impl Source code
reorder_names Source code
shared_groups Source code
shuffle_impl Source code
sorting Man page
subtract_impl Source code
tbl_genome Man page Source code
tbl_interval Man page Source code
trbl_genome Man page Source code
trbl_interval Man page Source code
valr Man page
valr-package Man page Man page
valr_example Man page Source code
values Man page Source code
values_unique Man page Source code

Files

inst
inst/CITATION
inst/extdata
inst/extdata/mm9.bed12.gz
inst/extdata/hg19.refGene.chr22.bed.gz
inst/extdata/3fields.bed.gz
inst/extdata/hg19.snps147.chr22.bed.gz
inst/extdata/12fields.bed.gz
inst/extdata/sample.broadPeak.gz
inst/extdata/sample.narrowPeak.gz
inst/extdata/hg19.chrom.sizes.gz
inst/extdata/test.vcf.gz
inst/extdata/hg19.rmsk.chr22.bed.gz
inst/extdata/hela.h3k4.chip.bg.gz
inst/extdata/6fields.bed.gz
inst/extdata/test.bg.gz
inst/extdata/genome.txt.gz
inst/extdata/genes.hg19.chr22.bed.gz
inst/doc
inst/doc/interval-stats.R
inst/doc/valr.Rmd
inst/doc/valr.html
inst/doc/interval-stats.Rmd
inst/doc/interval-stats.html
inst/doc/valr.R
inst/include
inst/include/valr.h
inst/include/dplyr.h
inst/include/random.h
inst/include/intervals.h
inst/include/solaris
inst/include/solaris/solaris.h
inst/include/group_apply.h
inst/include/tools
inst/include/tools/delete_all.h
inst/include/tools/SlicingIndex.h
inst/include/tools/SymbolMap.h
inst/include/tools/LazyDots.h
inst/include/tools/wrap_subset.h
inst/include/tools/hash.h
inst/include/tools/Encoding.h
inst/include/tools/tools.h
inst/include/tools/match.h
inst/include/tools/DotsOf.h
inst/include/tools/ShrinkableVector.h
inst/include/tools/get_single_class.h
inst/include/tools/get_all_second.h
inst/include/tools/all_na.h
inst/include/tools/pointer_vector.h
inst/include/tools/complex.h
inst/include/tools/collapse.h
inst/include/tools/StringUTF8.h
inst/include/tools/Call.h
inst/include/tools/FilteredListOf.h
inst/include/genome.h
inst/include/IntervalTree.h
inst/include/dplyr
inst/include/dplyr/CharacterVectorOrderer.h
inst/include/dplyr/tbl_cpp.h
inst/include/dplyr/subset_visitor.h
inst/include/dplyr/DataFrameColumnVisitor.h
inst/include/dplyr/visitor_set
inst/include/dplyr/visitor_set/VisitorSetLess.h
inst/include/dplyr/visitor_set/VisitorEqualPredicate.h
inst/include/dplyr/visitor_set/VisitorSetHash.h
inst/include/dplyr/visitor_set/VisitorSetEqualPredicate.h
inst/include/dplyr/visitor_set/VisitorSetEqual.h
inst/include/dplyr/visitor_set/VisitorSetIndexMap.h
inst/include/dplyr/visitor_set/VisitorHash.h
inst/include/dplyr/visitor_set/visitor_set.h
inst/include/dplyr/visitor_set/VisitorSetGreater.h
inst/include/dplyr/visitor_set/VisitorSetHasher.h
inst/include/dplyr/visitor_set/VisitorSetGreaterPredicate.h
inst/include/dplyr/visitor_set/VisitorSetLessPredicate.h
inst/include/dplyr/visitor_set/VisitorSetIndexSet.h
inst/include/dplyr/NamedListAccumulator.h
inst/include/dplyr/EmptySubset.h
inst/include/dplyr/Result
inst/include/dplyr/Result/DelayedReducer.h
inst/include/dplyr/Result/GroupedHybridCall.h
inst/include/dplyr/Result/Count.h
inst/include/dplyr/Result/LazyRowwiseSubsets.h
inst/include/dplyr/Result/all.h
inst/include/dplyr/Result/min.h
inst/include/dplyr/Result/Count_Distinct.h
inst/include/dplyr/Result/DelayedProcessor.h
inst/include/dplyr/Result/max.h
inst/include/dplyr/Result/Rank.h
inst/include/dplyr/Result/Var.h
inst/include/dplyr/Result/Result.h
inst/include/dplyr/Result/GroupedCallProxy.h
inst/include/dplyr/Result/Processor.h
inst/include/dplyr/Result/Sum.h
inst/include/dplyr/Result/CumMin.h
inst/include/dplyr/Result/In.h
inst/include/dplyr/Result/Mutater.h
inst/include/dplyr/Result/CumMax.h
inst/include/dplyr/Result/Lead.h
inst/include/dplyr/Result/is_smaller.h
inst/include/dplyr/Result/RowwiseSubset.h
inst/include/dplyr/Result/VectorSliceVisitor.h
inst/include/dplyr/Result/Mean.h
inst/include/dplyr/Result/CumSum.h
inst/include/dplyr/Result/CallProxy.h
inst/include/dplyr/Result/Sd.h
inst/include/dplyr/Result/Lag.h
inst/include/dplyr/Result/Everything.h
inst/include/dplyr/Result/GroupedCallReducer.h
inst/include/dplyr/Result/LazyGroupedSubsets.h
inst/include/dplyr/Result/ResultSet.h
inst/include/dplyr/Result/CallElementProxy.h
inst/include/dplyr/Result/ConstantResult.h
inst/include/dplyr/Result/CallbackProcessor.h
inst/include/dplyr/Result/factories.h
inst/include/dplyr/Result/LazySubsets.h
inst/include/dplyr/Result/GroupedSubset.h
inst/include/dplyr/SubsetVectorVisitor.h
inst/include/dplyr/vector_class.h
inst/include/dplyr/DataFrameVisitors.h
inst/include/dplyr/GroupedDataFrame.h
inst/include/dplyr/JoinVisitor.h
inst/include/dplyr/comparisons.h
inst/include/dplyr/config.h
inst/include/dplyr/workarounds.h
inst/include/dplyr/SubsetVectorVisitorImpl.h
inst/include/dplyr/DataFrameJoinVisitors.h
inst/include/dplyr/VectorVisitor.h
inst/include/dplyr/RowwiseDataFrame.h
inst/include/dplyr/DataFrameColumnSubsetVisitor.h
inst/include/dplyr/DataFrameSubsetVisitors.h
inst/include/dplyr/FullDataFrame.h
inst/include/dplyr/Gatherer.h
inst/include/dplyr/SummarisedVariable.h
inst/include/dplyr/white_list.h
inst/include/dplyr/workarounds
inst/include/dplyr/workarounds/static_assert.h
inst/include/dplyr/comparisons_different.h
inst/include/dplyr/BoolResult.h
inst/include/dplyr/Order.h
inst/include/dplyr/Replicator.h
inst/include/dplyr/DataFrameVisitorsIndexMap.h
inst/include/dplyr/OrderVisitorImpl.h
inst/include/dplyr/visitor.h
inst/include/dplyr/registration.h
inst/include/dplyr/train.h
inst/include/dplyr/MatrixColumnVisitor.h
inst/include/dplyr/MatrixColumnSubsetVectorVisitor.h
inst/include/dplyr/JoinVisitorImpl.h
inst/include/dplyr/DataFrameVisitorsIndexSet.h
inst/include/dplyr/OrderVisitor.h
inst/include/dplyr/VectorVisitorImpl.h
inst/include/dplyr/check_supported_type.h
inst/include/dplyr/DataFrameAble.h
inst/include/dplyr/Collecter.h
inst/include/dplyr/MultipleVectorVisitors.h
tests
tests/testthat.R
tests/testthat
tests/testthat/test_utils.R
tests/testthat/test_merge.r
tests/testthat/test_read_bed.r
tests/testthat/test_tbls.r
tests/testthat/test-db.r
tests/testthat/test_bed12_to_exons.r
tests/testthat/test_makewindows.r
tests/testthat/test_random.r
tests/testthat/test_intersect.r
tests/testthat/test_glyph.r
tests/testthat/test_map.r
tests/testthat/test_spacing.r
tests/testthat/test_sort.r
tests/testthat/test_shuffle.r
tests/testthat/test-style.r
tests/testthat/test_absdist.r
tests/testthat/test_read_vcf.r
tests/testthat/test_genome.r
tests/testthat/test_fisher.r
tests/testthat/test_window.r
tests/testthat/helper-astyle.r
tests/testthat/test_closest.r
tests/testthat/test_slop.r
tests/testthat/test_jaccard.r
tests/testthat/test_subtract.r
tests/testthat/test_complement.r
tests/testthat/test_projection.r
tests/testthat/test_flank.r
tests/testthat/test_shift.r
tests/testthat/test_reldist.R
tests/testthat/test_cluster.r
tests/testthat/test_coverage.r
tests/testthat/test_strands.r
src
src/reldist.cpp
src/Makevars
src/random.cpp
src/intersect.cpp
src/absdist.cpp
src/coverage.cpp
src/shuffle.cpp
src/complement.cpp
src/subtract.cpp
src/Makevars.win
src/init.c
src/RcppExports.cpp
src/closest.cpp
src/merge.cpp
NAMESPACE
NEWS.md
R
R/sorting.r
R/globals.r
R/bed_absdist.r
R/read_genome.r
R/read_bed.r
R/bed_random.r
R/db.r
R/bed_makewindows.r
R/bed_window.r
R/bed_coverage.R
R/strands.r
R/bed_shift.r
R/bed_slop.r
R/bed_fisher.r
R/bed_projection.r
R/bed_intersect.r
R/read_vcf.r
R/spacing.r
R/utils.r
R/valr.r
R/bed_merge.r
R/RcppExports.R
R/bed12_to_exons.r
R/bed_reldist.r
R/tbls.r
R/bed_jaccard.r
R/bed_subtract.r
R/bed_closest.r
R/bed_glyph.r
R/bed_complement.r
R/bed_cluster.r
R/bed_map.r
R/bed_flank.r
R/bed_shuffle.r
vignettes
vignettes/valr.Rmd
vignettes/interval-stats.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/trbl_genome.Rd
man/bed_coverage.Rd
man/bed_cluster.Rd
man/bed_slop.Rd
man/trbl_interval.Rd
man/bed_intersect.Rd
man/bed_shift.Rd
man/interval_spacing.Rd
man/bed_complement.Rd
man/figures
man/figures/logo.png
man/bed_sort.Rd
man/is.tbl_genome.Rd
man/bed_subtract.Rd
man/tbl_interval.Rd
man/db.Rd
man/bed_projection.Rd
man/valr.Rd
man/bed_makewindows.Rd
man/bed_fisher.Rd
man/read_genome.Rd
man/tbl_genome.Rd
man/bed_merge.Rd
man/read_bed.Rd
man/bed_shuffle.Rd
man/sorting.Rd
man/bed_window.Rd
man/bed_map.Rd
man/bed_reldist.Rd
man/bed_flank.Rd
man/bed12_to_exons.Rd
man/bed_random.Rd
man/bed_jaccard.Rd
man/flip_strands.Rd
man/bed_glyph.Rd
man/bed_closest.Rd
man/is.tbl_interval.Rd
man/bed_absdist.Rd
man/valr_example.Rd
man/read_vcf.Rd
man/bound_intervals.Rd
LICENSE
valr documentation built on May 19, 2017, 7:20 a.m.

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