dinamic: annot.file – R documentation

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annot.file

A Cytoband Annotation Data Frame

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

data(annot.file)

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

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

dinamic

DiNAMIC A Method To Analyze Recurrent DNA Copy Number Aberrations in Tumors

v1.0

GPL-2

Authors

Vonn Walter, Andrew B. Nobel, and Fred A. Wright

Initial release

2011-10-24