getGaps: get gaps for a stepping transformed GRanges object

In lawremi/biovizBase: Basic graphic utilities for visualization of genomic data.

Description

Get gaps for a stepping transformed GRanges object, for visualization purpose. So a extra "stepping" column is required. Please see details below for motivation.

Usage

## S4 method for signature 'GRanges'
getGaps(obj, group.name = NULL, facets = NULL)

Arguments

obj	A GRanges object.
group.name	group name, such as transcript ID, this is the group method within each panel of facets and gaps will be computed for each group of intervals.
facets	formula used for creating graphics, all variables must be present in the data.

Details

Since faceting is a subset and group process in visualization stage, some statistical computation need to be taken place after that. This leaves some computation like computing gaps hard based on solely GRanges object. Extra information like facets formula and group method would help to generate gaps which make sure they are aligned on the same level and within the same panel for grouped intervals. facets variables will be added to gaps GRanges along with group.name.

Value

A GRanges object representing gaps and for each row, the "stepping" column help later visualization and make sure gaps and intervals they are generated from are showed on the expected place.

Author(s)

Tengfei Yin

Examples

set.seed(1)
N <- 100
library(GenomicRanges)
gr <- GRanges(seqnames = 
              sample(c("chr1", "chr2", "chr3"),
                     size = N, replace = TRUE),
              IRanges(
                      start = sample(1:300, size = N, replace = TRUE),
                      width = sample(70:75, size = N,replace = TRUE)),
              strand = sample(c("+", "-", "*"), size = N, 
                replace = TRUE),
              value = rnorm(N, 10, 3), score = rnorm(N, 100, 30),
              sample = sample(c("Normal", "Tumor"), 
                size = N, replace = TRUE),
              pair = sample(letters, size = N, 
                replace = TRUE))

grl <- splitByFacets(gr, sample ~ seqnames)
gr <- unlist(endoapply(grl, addStepping))
gr.gaps <- getGaps(gr, group.name = "stepping", facets = sample ~ seqnames)

lawremi/biovizBase documentation built on Dec. 21, 2021, 9:42 a.m.