Tools for working with and comparing sets of points and intervals.

Author | Richard Bourgon <bourgon.richard@gene.com> |

Date of publication | 2013-03-09 04:37:26 |

Maintainer | Richard Bourgon <bourgon.richard@gene.com> |

License | Artistic-2.0 |

Version | 0.14.0 |

**as.matrix.Intervals:** Extract matrix of endpoints

**c.Intervals:** Combine different interval matrix objects

**close_intervals-methods:** Re-represent integer intervals with open or closed endpoints

**clusters-methods:** Identify clusters in a collection of positions or intervals

**distance_to_nearest-methods:** Compute distance to nearest position in a set of intervals

**empty-methods:** Identify empty interval rows

**expand-methods:** Expand or contract intervals

**interval_complement-methods:** Compute the complement of a set of intervals

**interval_difference-methods:** Compute set difference

**interval_included-methods:** Assess inclusion of one set of intervals with respect to...

**interval_intersection-methods:** Compute the intersection of one or more sets of intervals

**interval_overlap-methods:** Assess overlap from one set of intervals to another

**Intervals-class:** Classes "Intervals" and "Intervals_full"

**intervals-package:** Tools for working with points and intervals

**Intervals_virtual-class:** Class "Intervals_virtual"

**Intervals_virtual_or_numeric-class:** Class "Intervals_virtual_or_numeric"

**interval_union-methods:** Compute the union of intervals in one or more interval...

**plot.Intervals:** Plotting methods for interval objects

**reduce-methods:** Compactly re-represent the points in a set of intervals

**sgd:** Yeast gene model sample data

**size-methods:** Compute interval sizes

**split.Intervals_virtual:** Split an intervals object according to a factor

**which_nearest-methods:** Identify nearest member(s) in a set of intervals

adjust_closure | Man page |

adjust_closure,Intervals_full-method | Man page |

adjust_closure,Intervals-method | Man page |

as.matrix | Man page |

as.matrix.Intervals_virtual | Man page |

as.matrix,Intervals_virtual-method | Man page |

c | Man page |

c.Intervals | Man page |

c.Intervals_full | Man page |

closed | Man page |

closed<- | Man page |

closed<-,Intervals_full-method | Man page |

closed<-,Intervals-method | Man page |

closed,Intervals_virtual-method | Man page |

closed,Intervals_virtual-method | Man page |

close_intervals | Man page |

close_intervals,Intervals_virtual-method | Man page |

clusters | Man page |

clusters,Intervals_virtual-method | Man page |

clusters,numeric-method | Man page |

coerce,Intervals_full,Intervals-method | Man page |

coerce,Intervals,Intervals_full-method | Man page |

coerce,Intervals_virtual,character-method | Man page |

contract | Man page |

contract,Intervals_virtual-method | Man page |

distance_to_nearest | Man page |

distance_to_nearest,Intervals_virtual_or_numeric,Intervals_virtu | Man page |

empty | Man page |

empty,Intervals_full-method | Man page |

empty,Intervals-method | Man page |

expand | Man page |

expand,Intervals_virtual-method | Man page |

head,Intervals_virtual-method | Man page |

initialize,Intervals_full-method | Man page |

initialize,Intervals-method | Man page |

initialize,Intervals_virtual-method | Man page |

interval_complement | Man page |

interval_complement,Intervals_virtual-method | Man page |

interval_difference | Man page |

interval_difference,Intervals_virtual,Intervals_virtual-method | Man page |

interval_included | Man page |

interval_included,Intervals_full,Intervals_full-method | Man page |

interval_included,Intervals,Intervals-method | Man page |

interval_intersection | Man page |

interval_intersection,Intervals_virtual-method | Man page |

interval_intersection,missing-method | Man page |

interval_overlap | Man page |

interval_overlap,ANY,missing-method | Man page |

interval_overlap,Intervals_virtual_or_numeric,Intervals_virtual_ | Man page |

interval_overlap,missing,ANY-method | Man page |

intervals | Man page |

Intervals | Man page |

[<-,Intervals,ANY,missing,Intervals_virtual-method | Man page |

Intervals-class | Man page |

Intervals_full | Man page |

[<-,Intervals_full,ANY,missing,Intervals_virtual-method | Man page |

Intervals_full-class | Man page |

[,Intervals_full-method | Man page |

[,Intervals-method | Man page |

intervals-package | Man page |

Intervals_virtual-class | Man page |

Intervals_virtual_or_numeric-class | Man page |

interval_union | Man page |

interval_union,Intervals_virtual-method | Man page |

interval_union,missing-method | Man page |

is.na,Intervals_virtual-method | Man page |

open_intervals | Man page |

open_intervals,Intervals_virtual-method | Man page |

plot | Man page |

plot.Intervals | Man page |

plot,Intervals,ANY-method | Man page |

plot.Intervals_full | Man page |

plot,Intervals_full,ANY-method | Man page |

plot,Intervals_full,missing-method | Man page |

plot,Intervals,missing-method | Man page |

reduce | Man page |

reduce,Intervals_virtual-method | Man page |

sgd | Man page |

show,Intervals_virtual-method | Man page |

size | Man page |

size,Intervals_full-method | Man page |

size,Intervals-method | Man page |

split | Man page |

split.Intervals_virtual | Man page |

split,Intervals_virtual-method | Man page |

tail,Intervals_virtual-method | Man page |

t,Intervals_virtual-method | Man page |

type | Man page |

type<- | Man page |

type<-,Intervals_virtual-method | Man page |

type,Intervals_virtual-method | Man page |

which_nearest | Man page |

which_nearest,Intervals_virtual,Intervals_virtual-method | Man page |

which_nearest,Intervals_virtual,numeric-method | Man page |

which_nearest,numeric,Intervals_virtual-method | Man page |

which_nearest,numeric,numeric-method | Man page |

intervals

intervals/man

intervals/man/interval_complement-methods.Rd
intervals/man/Intervals-class.Rd
intervals/man/c.Intervals.Rd
intervals/man/reduce-methods.Rd
intervals/man/distance_to_nearest-methods.Rd
intervals/man/expand-methods.Rd
intervals/man/empty-methods.Rd
intervals/man/interval_union-methods.Rd
intervals/man/as.matrix.Intervals.Rd
intervals/man/intervals-package.Rd
intervals/man/clusters-methods.Rd
intervals/man/Intervals_virtual-class.Rd
intervals/man/interval_difference-methods.Rd
intervals/man/size-methods.Rd
intervals/man/plot.Intervals.Rd
intervals/man/Intervals_virtual_or_numeric-class.Rd
intervals/man/interval_overlap-methods.Rd
intervals/man/interval_included-methods.Rd
intervals/man/sgd.Rd
intervals/man/interval_intersection-methods.Rd
intervals/man/close_intervals-methods.Rd
intervals/man/which_nearest-methods.Rd
intervals/man/split.Intervals_virtual.Rd
intervals/DESCRIPTION

intervals/src

intervals/src/which_nearest.cpp

intervals/src/reduce.cpp

intervals/src/Endpoint.cpp

intervals/src/Endpoint.h

intervals/src/plot_overlap.cpp

intervals/tests

intervals/tests/intervals_test_code.R

intervals/data

intervals/data/sgd.rdata

intervals/NAMESPACE

intervals/inst

intervals/inst/doc

intervals/inst/doc/intervals_overview.pdf

intervals/inst/doc/intervals_overview.Rnw

intervals/R

intervals/R/size-methods.R
intervals/R/close_intervals-methods.R
intervals/R/clusters.R
intervals/R/interval_difference-methods.R
intervals/R/which_nearest-methods.R
intervals/R/empty-methods.R
intervals/R/t-methods.R
intervals/R/as.matrix.R
intervals/R/show-methods.R
intervals/R/interval_union-methods.R
intervals/R/reduce-methods.R
intervals/R/interval_complement-methods.R
intervals/R/interval_intersection-methods.R
intervals/R/closed-methods.R
intervals/R/head-methods.R
intervals/R/is.na-methods.R
intervals/R/interval_overlap-methods.R
intervals/R/Intervals-class.R
intervals/R/plot.Intervals_virtual.R
intervals/R/distance_to_nearest-methods.R
intervals/R/expand-methods.R
intervals/R/interval_included-methods.R
intervals/R/type-methods.R
intervals/R/c.R
intervals/R/split.R
intervals/NEWS

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.