which_nearest-methods {girafe} | R Documentation

## Methods for function 'which_nearest' and genome intervals

### Description

For each genome interval in one set, finds the nearest interval in a second set of genome intervals.

### Value

a `data.frame` with a number of rows equal to the number of intervals in argument `from`. The elements of the data.frame are:

`distance_to_nearest` | numeric; distance to nearest interval from object `to`. Is 0 if the current interval in object `from` did overlap one or more intervals in object `to`
`which_nearest` | list; each list element are the indices or the intervals in object `to` that have the closest distance to the current interval in object `from`
`which_overlap` | list; each list element are the indices or the intervals in object `to` that do overlap with the current interval in object `from`

### Methods

Currently, the package girafe contains method implementations for the first object (Argument: `from`) being of any of the classes “AlignedGenomeIntervals”,“Genome_intervals” or “Genome_intervals_stranded”. The second object (Argument: `to`) has be of class “Genome_intervals_stranded” or “Genome_intervals”.

### Note

If the supplied objects are stranded, as it is the case with objects of classes ‘AlignedGenomeIntervals’ and ‘Genome_intervals_stranded’, then the overlap and distance is solely computed between intervals on the same strand.

For objects of class ‘Genome_intervals’, overlap and distances are computed regardless of strand information.

### Author(s)

Joern Toedling

### See Also

`which_nearest`

### Examples

      ### process aligned reads
      exDir <- system.file("extdata", package="girafe")
      exA   <- readAligned(dirPath=exDir, type="Bowtie",
        pattern="aravinSRNA_23_no_adapter_excerpt_mm9_unmasked.bwtmap")
      exAI <- as(exA, "AlignedGenomeIntervals")

      ## load annotated genome features
      load(file.path(exDir, "mgi_gi.RData"))

      ## subset for sake of speed:
      A <- exAI[is.element(seqnames(exAI), c("chrX","chrY"))]
      G <- mgi.gi[is.element(seqnames(mgi.gi), c("chrX","chrY"))]

      ## find nearest annotated feature for each AlignedGenomeInterval
      WN <- which_nearest(A, G)
      dim(WN); tail(WN)

      ## notice the difference to:
      tail(which_nearest(as(A, "Genome_intervals"), G))
      # the last interval in A is located antisense to a gene,
      # but not overlapping anything on the same strand

[Package girafe version 1.44.0 Index]