reduceKeepAttr {ORFik} | R Documentation

## Reduce GRanges / GRangesList

### Description

Extends function [GenomicRanges::reduce()] by trying to keep names and meta columns, if it is a GRangesList. It also does not loose sorting for GRangesList, since original reduce sorts all by ascending. If keep.names == FALSE, it's just the normal GenomicRanges::reduce with sorting negative strands descending for GRangesList.

### Usage

    reduceKeepAttr(grl, keep.names = FALSE, drop.empty.ranges = FALSE,
      min.gapwidth = 1L, with.revmap = FALSE, with.inframe.attrib = FALSE,
      ignore.strand = FALSE)

### Arguments

`grl` | a `GRangesList` or GRanges object
`keep.names` | (FALSE) keep the names and meta columns of the GRangesList
`drop.empty.ranges` | (FALSE) if a group is empty (width 0), delete it.
`min.gapwidth` | (1L) how long gap can it be to say they belong together
`with.revmap` | (FALSE) return info on which mapped to which
`with.inframe.attrib` | (FALSE) For internal use.
`ignore.strand` | (FALSE), can different strands be reduced together.

### Value

A reduced GRangesList

### Examples

    ORF <- GRanges(seqnames = "1",
                   ranges = IRanges(start = c(1, 2, 3), end = c(1, 2, 3)),
                   strand = "+")
    # For GRanges
    reduceKeepAttr(ORF, keep.names = TRUE)
    # For GRangesList
    grl <- GRangesList(tx1_1 = ORF)
    reduceKeepAttr(grl, keep.names = TRUE)

[Package ORFik version 1.0.0 Index]