selectAlnRegionsHelpers: Helper functions for selectAlnRegions

In HLindsay/CrispRVariants: Tools for counting and visualising mutations in a target location

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)

HLindsay/CrispRVariants documentation built on May 28, 2019, 12:40 p.m.