List the available chromosome

List the chromosomes available in the file.

listChromosomes(file, format = c("hic", "cool"))

Arguments

file

character(1). File name of .hic or .cool/.mcool/.scool

format

character(1). File format, "hic" or "cool".

Examples

hicfile <- system.file("extdata", "test_chr22.hic", package="trackViewer")
listChromosomes(hicfile)
#>    index name    length
#> 1      1    1 249250621
#> 2     10   10 135534747
#> 3     11   11 135006516
#> 4     12   12 133851895
#> 5     13   13 115169878
#> 6     14   14 107349540
#> 7     15   15 102531392
#> 8     16   16  90354753
#> 9     17   17  81195210
#> 10    18   18  78077248
#> 11    19   19  59128983
#> 12     2    2 243199373
#> 13    20   20  63025520
#> 14    21   21  48129895
#> 15    22   22  51304566
#> 16     3    3 198022430
#> 17     4    4 191154276
#> 18     5    5 180915260
#> 19     6    6 171115067
#> 20     7    7 159138663
#> 21     8    8 146364022
#> 22     9    9 141213431
#> 23     0  ALL   3095693
#> 24    25   MT     16569
#> 25    23    X 155270560
#> 26    24    Y  59373566
coolfile <- system.file("extdata", "test.mcool", package="trackViewer")
listChromosomes(coolfile, format="cool")
#> [1] "chr1" "chr2"