syncRangesDir: Synchronize orientation of genomic ranges given the desired...

In daewoooo/SVbyEye: Visualization of genomic structural variants

Synchronize orientation of genomic ranges given the desired majority direction.

Description

This function takes a set of ranges in GRanges-class or GRangesList-class object and return the same ranges in same class object such that total length of plus (direct, '+') and minus (minus, '-') . oriented ranges meet the user defined 'majority.strand' orientation.

Usage

syncRangesDir(ranges, majority.strand = "+", strand.only = FALSE)

Arguments

ranges	A GRanges object.
majority.strand	A desired majority strand directionality to be reported.
strand.only	If set to TRUE simple character string of strand directionality ('+', '-') is reported.

Value

A GRanges-class or GRangesList-class object.

Author(s)

David Porubsky

Examples

## Define test genomic ranges to synchronize directionality ##
test.gr <- GenomicRanges::GRanges(
    seqnames = "test",
    ranges = IRanges::IRanges(
        start = c(1, 200, 300),
        end = c(200, 300, 500)
    ), strand = c("-", "+", "-")
)
syncRangesDir(ranges = test.gr, majority.strand = "+")

daewoooo/SVbyEye documentation built on Oct. 15, 2024, 6:12 a.m.