closest.regions: Find closets regions to reference regions.

View source: R/closest.regions.R

closest.regionsR Documentation

Find closets regions to reference regions.

Description

This tools return the closest upstream and downstream regions from a reference region.

Usage

closest.regions(
  reference.regions,
  reference.regions.table.name = "referenceRegions",
  target.regions,
  export.table.file = NULL,
  return.table = TRUE,
  collapse.regions = FALSE,
  verbose = TRUE
)

Arguments

reference.regions

A full path to a bed file or a data.frame in at least BED3 format with the regions to use as reference.

reference.regions.table.name

A string with the name to use for the group reference regions. By default "referenceRegions".

target.regions

A full path to a bed file or a data.frame in at least BED3 format with the regions to uses as targets.

export.table.file

A string with the full path for the file in which the table should be exported. By default NULL: not export.

return.table

Logical value to define whether the output table should be returned. By default TRUE.

collapse.regions

Logical value to define whether the partially overlapping regions should be collapsed or not. By default FALSE.

verbose

Logical value to define whether messages should be printed. By default TRUE.

Value

The function returns a data.frame composed of a triplicated chr-start-end-name table for reference.region, upstream.region and downstream.region, respectively.


sebastian-gregoricchio/Rseb documentation built on May 15, 2024, 5:45 a.m.