.invertKeepRanges {CrispRVariants} | R Documentation

## Helper functions for selectAlnRegions

### Description

(.invertKeepRanges) Internal CrispRVariants function used by seqsToPartialAlns for checking arguments and getting region to delete. Returns FALSE if no region to delete found, or region to be deleted is entire target.

(.checkRelativeLocs) Shift keep to start at 1 if it is within the target

(.adjustRelativeInsLocs) Internal CrispRVariants function for shifting insertion locations relative to the target region when removing a segment of the alignments. Note that this function does not do input checking but assumes this has been done upstream. Insertions at the left border of a gap region are removed.

(.offsetIndices) Get indices of a vector grouped by "x", cumulatively adding offsets to each group according to "offset"

### Usage

    .invertKeepRanges(target, keep)

    .checkRelativeLocs(target, keep)

    .adjustRelativeInsLocs(target, keep, starts, gap_nchars)

    .offsetIndices(x, offset)

### Arguments

`target` | The complete region spanned by the alignments (GRanges)
`keep` | Region to display, relative to the target region, i.e. not genomic coords (IRanges or GRanges)
`starts` | numeric(n) Insertion locations. When plotting, the insertion symbol appears at the left border of the start location.
`gap_nchars` | character(n) Number of letters added to when joining segments before each region in keep. If first base of keep is 1, the first entry of gap_nchars should be 0.
`x` | A vector of group lengths
`offset` | A vector of offset lengths matching x

### Value

Gaps between keep (IRanges), or FALSE if no gap ranges found

insertion_sites (data.frame) with modified start column

### Author(s)

Helen Lindsay

### Examples

    CrispRVariants:::.offsetIndices(rep(2,5), c(0:4)*10)

[Package CrispRVariants version 1.15.0 Index]