Read/parse chromInfo data from a data frame/file/UCSC database
Read/parse chromInfo data from a data frame/file/UCSC database
read.chromInfo(
chromInfo = system.file(package = "circlize", "extdata", "chromInfo.txt"),
species = NULL,
chromosome.index = usable_chromosomes(species),
sort.chr = TRUE)chromInfo |
Path of the chromInfo file or a data frame that already contains chromInfo 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 chromInfo data, sort the chromosome names and calculate the length of each chromosome. By default, it is human hg19 chromInfo data.
You can find the data structure for the chromInfo data from https://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.gz
dfData frame for chromInfo data (rows are sorted if sort.chr is set to TRUE)
chromosomeSorted chromosome names
chr.lenLength of chromosomes. Order are same as chromosome
data = read.chromInfo(species = "hg19")
data = read.chromInfo(chromInfo = system.file(package = "circlize", "extdata", "chromInfo.txt"))
chromInfo = read.table(system.file(package = "circlize", "extdata", "chromInfo.txt"),
colClasses = c("character", "numeric"), sep = "\t")
data = read.chromInfo(chromInfo = chromInfo)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.