mm10_gap: Gaps

In chromPlot: Global visualization tool of genomic data

Description

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

Usage

data(mm10_gap)

Format

A data frame with 686 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 (Dec. 2011, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)) of the mouse 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 mouse genome.

Examples

data(mm10_gap)
## maybe str(mm10_gap) ; plot(mm10_gap) ...

Example output

Loading required package: biomaRt
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb

chromPlot documentation built on Nov. 8, 2020, 5:12 p.m.