addStepping-method {biovizBase} | R Documentation

## Adding disjoint levels to a GenomicRanges object

### Description

Adding disjoint levels to a GenomicRanges object

### Usage

    ## S4 method for signature 'GenomicRanges'
    addStepping(obj, group.name, extend.size = 0,
                           fix = "center",
                           group.selfish = TRUE)

### Arguments

`obj` | A GenomicRanges object
`group.name` | Column name in the elementMetadata which specify the grouping information of all the entries. If provided, this will make sure all intervals belong to the same group will try to be on the same level and nothing falls in between.
`extend.size` | Adding invisible buffered region to the GenomicRanges object, if it's 10, then adding 5 at both end. This make the close neighbors assigned to the different levels and make your eyes easy to identify.
`fix` | "start", "end", or "center"(default) passed to `resize`, denoting what to use as an anchor for each element of obj, and add extend.size to it's current width.
`group.selfish` | Passed to `addStepping`, control whether to show each group as unique level or not. If set to `FALSE`, if two groups are not overlapped with each other, they will probably be layout in the same level to save space.

### Details

This is a tricky question, for example, pair-end RNA-seq data could be represented as two set of GenomicRanges object, one indicates the read, one indicates the junction. At the same time, we need to make sure pair-ended read are shown on the same level, and nothing falls in between. For better visualization of the data, we may hope to add invisible extended buffer to the reads, so closely neighbored reads will be on the different levels.

### Value

A modified GenmicRanges object with `stepping` as one column.

### Author(s)

Tengfei Yin

### Examples

    library(GenomicRanges)
    set.seed(1)
    N <- 500
    ## sample GRanges
    gr <- GRanges(seqnames =
                  sample(c("chr1", "chr2", "chr3", "chrX", "chrY"),
                         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),
                  group = sample(c("Normal", "Tumor"),
                    size = N, replace = TRUE),
                  pair = sample(letters, size = N,
                    replace = TRUE))

    ## grouping and extending
    head(addStepping(gr))
    head(addStepping(gr, group.name = "pair"))
    gr.close <- GRanges(c("chr1", "chr1"), IRanges(c(10, 20), width = 9))
    addStepping(gr.close)
    addStepping(gr.close, extend.size = 5)

[Package biovizBase version 1.40.0 Index]