Read/parse cytoband data from a data frame/file/UCSC database
Read/parse cytoband data from a data frame/file/UCSC database
read.cytoband(
cytoband = system.file(package = "circlize", "extdata", "cytoBand.txt"),
species = NULL,
chromosome.index = usable_chromosomes(species),
sort.chr = TRUE)cytoband |
Path of the cytoband file or a data frame that already contains cytoband data |
species |
Abbreviations of species. e.g. hg19 for human, mm10 for mouse. If this
value is specified, the function will download |
chromosome.index |
subset of chromosomes, also used to reorder chromosomes. |
sort.chr |
Whether chromosome names should be sorted (first sort by numbers then by letters).
If |
The function read the cytoband data, sort the chromosome names and calculate the length of each chromosome. By default, it is human hg19 cytoband data.
You can find the data structure of the cytoband data from https://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/cytoBand.txt.gz
dfData frame for cytoband data (rows are sorted if sort.chr is set to TRUE)
chromosomeSorted chromosome names
chr.lenLength of chromosomes. Orders are same as chromosome
data = read.cytoband(species = "hg19")
data = read.cytoband(cytoband = system.file(package = "circlize", "extdata", "cytoBand.txt"))
cytoband = read.table(system.file(package = "circlize", "extdata", "cytoBand.txt"),
colClasses = c("character", "numeric", "numeric", "character", "character"), sep = "\t")
data = read.cytoband(cytoband = cytoband)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.