hg_gap {chromPlot} | R Documentation

## Human Gap

### Description

This track depicts gaps in the assembly of the human genome.

### Usage

    data(hg_gap)

### Format

A data frame with 457 observations on the following 4 variables.

`Chrom`

  a character vector

`Start`

  a numeric vector

`End`

  a numeric vector

`Name`

  a character vector

### Details

This track depicts gaps in the assembly of human genome. Gaps are represented as black boxes in this track. This assembly contains the following principal types of gaps: (In this context, a contig is a set of overlapping sequence reads.) Clone - gaps between clones (114 gaps). Contig - gaps between map contigs, various sizes (104 gaps). Telomere - 42 gaps for telomeres (100,000 Ns) Centromere - 20 gaps for centromeres (size: 2,890,000 Ns) Short_arm - 21 gaps for the short arm (10,000 Ns) at base positions 100, 001-110,000 of each chromosome. other - sequence of Ns in the assembly that were not marked as gaps in the AGP assembly definition file, various sizes (384 gaps). Fragment - a single gap of 31 bases in chrX_GL456233_random.

### Value

data.frame that contain the gaps in the assembly of the human genome.

### Examples

    data(hg_gap)
    ## maybe str(hg_gap) ; plot(hg_gap) ...

[Package chromPlot version 1.12.0 Index]