makeBandInfo {iGenomicViewer}R Documentation

Function for creating bandinfo object

Description

This function creates a bandinfo object that contains genomic location information for chromosomes, arms, broad bands, and fine bands.

Usage

makeBandInfo(file,
             chrom.levels, 
             file.sep="\t",
             autosomes=1:22,
             X.chrom = 23, 
             Y.chrom = 24,
             chr.dx = 1,
             band.dx = 4,
             start.dx = 2,
             stop.dx = 3,                         
             returnVl=TRUE,
             saveFile=FALSE,
             saveName = "BandInfo.RData",
             ...)

Arguments

file path name of file
chrom.levels vector indicating how the chrom column in the file is represented. i.e chr1, chrom1, 1, etc.
file.sep seperation character for file
autosomes numeric vector listing autosomes. defaults to human 1:22
X.chrom numeric indication of x chromosome. defaults to human 23
Y.chrom numeric indication of y chromosome. defaults to human 24
chr.dx column in file that represents the chromosome
band.dx column in file that represents the band. assumed to be without chromosome i.e. q11, p13.1, etc.
start.dx column in file that represents the starting genomic location of band region
stop.dx column in file that represents the stopping genomic location of band region
returnVl logical indicating if object created should be returned
saveFile logical indicating if object created should be saved to a file
saveName if saveVl, path name of file
... additional arguments to the read.table function for reading the file

Details

This function is designed to make useful data.frames of starting and ending genomic locations for chromosomes, arms, broad.bands, and fine.bands. Each data.frame has five columns: the region (chrom, arm), label, lower, center, and upper. lower, center, and upper refer to genomic locations. label is the label that will be used for the region when plotting. The bandinfo object will also contain an offset object. This is a numeric vector of length equal to the number of chromsomes. It contains the numeric buffer that should be added to genomic locations given within chromosome to get the location with respect to the entire genome. These data.frames and indicies aid in graphing when utilizing the iGGV function.

Value

a bandinfo object that contains location information for chormosomes, arms, broad bands, and fine bands. see bandinfo for more details

Author(s)

Lori A. Shepherd

See Also

bandinfo, Band.Info, iGGV

Examples


#
# The following code will build the same object as data(Band.Info)
#

library("iGenomicViewer")

# writes out text files to use
writeExFiles()

# make object
band.info = makeBandInfo(file="cytoBand.txt", chrom.levels=c("chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22","chrX","chrY"), file.sep="\t", returnVl=TRUE, header=TRUE)


[Package iGenomicViewer version 2.4.6 Index]