biovizBase (version 1.20.0)

getGaps: get gaps for a stepping transformed GRanges object

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

"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.

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.

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.

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)