makeBandInfo {iGenomicViewer} | R Documentation |
This function creates a bandinfo object that contains genomic location information for chromosomes, arms, broad bands, and fine bands.
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", ...)
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 |
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.
a bandinfo object that contains location information for chormosomes, arms, broad bands, and fine bands. see bandinfo for more details
Lori A. Shepherd
# # 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)