makeCytoband: Find the Chromosome Arm for Each Marker

Description Usage Arguments Details Value Note Author(s) References Examples

View source: R/dinamic.R

Description

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.

Usage

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makeCytoband(marker.data, annot.file, reformat.annot = FALSE)

Arguments

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 quickLook and detailedLook.

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 annot.file needs to be reformatted. See "Note" for additional information.

Details

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)).

Value

A character vector of length m, where m is the number of markers.

Note

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.

Author(s)

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

Maintainer: <vwalter@email.unc.edu> Vonn Walter

References

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.

Examples

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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 

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