Description Usage Arguments Value

View source: R/IntersectionHelper.R

Given a GRangesList object, determine which items overlap each others.

1 | ```
build_intersect(grl, keep.signal = FALSE)
``` |

`grl` |
The GRangesList object whose elements need to be overlapped with each others. |

`keep.signal` |
Should the values of signal be kept? |

A list with the following elements:

- Regions
A GRanges object with all genomic ranges occupied by at least one item. All ranges are "flattened", so if two of the initial ranges overlapped each other imperfectly, they are combined into a single region spanning both of them.

- Matrix
A matrix, with

`ncol=`

the number of items in the initial GRangesList and`nrow=`

the total number of loci, which is equal to the length of`Regions`

. A value of 1 or more within the matrix indicates that the regions described by the column overlapped the region defined by the row.- List
A list of

`length(grl)`

numeric vectors indicating which indices of`Regions`

overlap with the given condition/protein. Useful to translate the regions into unique names for drawing venn diagrams.- Names
The names of the initial grl items, corresponding to the column names of

`Matrix`

and the names of the element of`List`

.- Length
The number of items in the initial GRangesList, corresponding to the number of columns in

`Matrix`

and the number of elements in`List`

.

ArnaudDroitLab/ef.utils documentation built on June 19, 2018, 8:26 p.m.

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