annot.file: A Cytoband Annotation Data Frame

Description Usage Format Source References Examples

Description

This four-column data frame contains cytoband annotation data that is used by the makeCytoband function. Each row corresponds to a distinct cytoband, and column 1 contains the chromosome number, column 2 contains the start position (in base pairs), column 3 contains the end position (in base pairs), and column 4 contains the cytoband name (e.g. p21.3). Additional columns may be present, but they are not used.

Usage

1

Format

A data frame with 811 observations on the following 4 variables.

Chr

The chromosome for the cytoband

Start

The start position (in base pairs) for the cytoband

End

The end position (in base pairs) for the cytoband

Band

The cytoband name (e.g. p13.1)

Source

The file cytoBand.txt.gz for the hg19 build can be downloaded from the UCSC Genome Browser at http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/. The format of cytoBand.txt differs from that of annot.file, but it can be used by the function makeCytoband if reformat.cytoband = TRUE.

References

Fujita P.A., Rhead B., Zweig A.S., et al., The UCSC Genome Browser database: update 2011, Nucleic Acids Res. (2010) 1 - 7 doi:10.1093/nar/gkq963.

Examples

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data(annot.file)
annot.file[1:10,]
#Produces the following output
#Chr    Start      End   Band
#1    1        0  2300000 p36.33
#2    1  2300000  5300000 p36.32
#3    1  5300000  7100000 p36.31
#4    1  7100000  9200000 p36.23
#5    1  9200000 12600000 p36.22
#6    1 12600000 16100000 p36.21
#7    1 16100000 20300000 p36.13
#8    1 20300000 23800000 p36.12
#9    1 23800000 27800000 p36.11
#10   1 27800000 30000000  p35.3

Example output

   Chr    Start      End   Band
1    1        0  2300000 p36.33
2    1  2300000  5300000 p36.32
3    1  5300000  7100000 p36.31
4    1  7100000  9200000 p36.23
5    1  9200000 12600000 p36.22
6    1 12600000 16100000 p36.21
7    1 16100000 20300000 p36.13
8    1 20300000 23800000 p36.12
9    1 23800000 27800000 p36.11
10   1 27800000 30000000  p35.3

dinamic documentation built on May 2, 2019, 9:18 a.m.