getAnnotationLevels: Assign each genomic range a non-overlapping level value

In daewoooo/SVbyEye: Visualization of genomic structural variants

Assign each genomic range a non-overlapping level value

Description

This function takes a set of genomic ranges in GRanges-class object and assign to each range a unique level such that each range or group of ranges (if 'annotation.group' is defined) resides on different levels.

Usage

getAnnotationLevels(
  annot.gr = NULL,
  offset = NULL,
  annotation.group = NULL,
  direction = "positive"
)

Arguments

annot.gr	A GRanges-class object with a set of ranges to report unique non-overlapping levels for.
offset	A numeric value from which unique annotation levels start from.
annotation.group	A name of an extra field present in 'annot.gr' to be used to report unique levels for a set of ranges that belong to the same group.
direction	Set to 'positive' or 'negative' to make sure reported levels are either decreasing or increasing from the defined 'offset' (default: 'positive').

Value

A numeric vector of unique levels corresponding to submitted ranges via 'annot.gr'.

Author(s)

David Porubsky

Examples

## Define random set of ranges grouped by gene name
test.gr1 <- GenomicRanges::GRanges(seqnames = 'target.region',
                ranges = IRanges::IRanges(start = c(19000000, 19030000, 19070000),
                                          end = c(19010000, 19050000, 19090000)))
test.gr1$ID <- 'gene1'
test.gr2 <- GenomicRanges::shift(test.gr1, shift = 10000)
test.gr2$ID <- 'gene2'
test.gr3 <- GenomicRanges::shift(test.gr1, shift = 90000)
test.gr3$ID <- 'gene3'
test.gr <- c(test.gr1, test.gr2, test.gr3)
## Obtain unique annotation levels grouped by ID
getAnnotationLevels(annot.gr = test.gr, offset = 1, annotation.group = 'ID')

daewoooo/SVbyEye documentation built on March 31, 2024, 8:58 a.m.