makeCytoband {dinamic}

Find the chromosome arm for each marker

Description

Find the chromosome arm for each marker

Usage

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 marker. 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.

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.

Examples

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
#   p    q 
#1147 2141