Find the Chromosome Arm for Each Marker
This function is used internally by DiNAMIC's peeling function. It finds the chromosome arm (p or q) for each marker in the matrix marker.data.
makeCytoband(marker.data, annot.file, reformat.annot = FALSE)
marker.data |
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 |
annot.file |
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. |
reformat.annot |
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
max(colSums(x)).
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: <vwalter@email.unc.edu> 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.
data(wilms.markers) data(annot.file) wilms.pq = makeCytoband(wilms.markers, annot.file) #A character vector of length 3288, and each entry is either #"p" or "q", depending on the chromosome arm of the given marker. table(wilms.pq) #Produces the following output: #wilms.pq #1147 2141
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