This function is used internally by DiNAMIC's
peeling function. It finds the chromosome arm (p or q) for each marker in the matrix
A two-column numeric matrix of marker position data for markers in the autosomes. Column 1 contains the chromosome number for each marker, and column 2 contains the position (in base pairs)
for each markers. This is a submatrix of the marker position matrix used by
A dataframe containing cytoband annotation for the autosomes. 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.
A logical value that indicates whether
DiNAMIC's peeling procedure is detailed in Bioinformatics (2011) 27(5) 678 - 685, and it is performed by the
peeling function. By construction, the peeling procedure only affects markers
in a given chromosome arm. This function is used internally by the
peeling function to restrict the peeling procedure to the chromosome arm containing the marker that corresponds to
A character vector of length m, where m is the number of markers.
A four-column cytoband annotation file called
annot.file is included in the package. However, users who wish to use other cytoband annotation files can
download five-column annotation files from the UCSC Genome Browser. For example, the file cytoBand.txt.gz for the hg19 build can be found at
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/. The entries in the first column of cytoBand.txt do not have the correct form, and this file also
contains cytoband annotation data for the X and Y chromosomes. Thus users should change
reformat.annot to TRUE when using these files.
Vonn Walter, Andrew B. Nobel, Fred A. Wright
Maintainer: <email@example.com> Vonn Walter
Walter, V., Nobel, A.B., and Wright, F.A., DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors, Bioinformatics (2011) 27(5) 678 - 685.
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