R: Read/parse chromInfo data from a data frame/file/UCSC...

read.chromInfo {circlize} | R Documentation

## Read/parse chromInfo data from a data frame/file/UCSC database

### Description

Read/parse chromInfo data from a data frame/file/UCSC database

### Usage

    read.chromInfo(chromInfo = system.file(package = "circlize",
        "extdata", "chromInfo.txt"), species = NULL, chromosome.index = NULL, sort.chr = TRUE)

### Arguments

`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 `chromInfo.txt.gz` from UCSC website automatically.
`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 `chromosome.index` is set, this argument is enforced to `FALSE`

### Details

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 http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/chromInfo.txt.gz

### Value

`df`

  Data frame for chromInfo data (rows are sorted if `sort.chr` is set to `TRUE`)

`chromosome`

  Sorted chromosome names

`chr.len`

  Length of chromosomes. Order are same as `chromosome`

### Examples

    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)

[Package circlize version 0.4.1 Index]