Transform a .cool file to a sparse upper triangular matrix for input into hic_loess

cooler2sparse(cooler)

Arguments

cooler	The plain text file from a .cool file loaded into an R data.frame object. See vignette for more details.

Value

A Sparse upper triangular matrix or a list of sparse upper triangular matrices. If the .cool file contains data for more than one chromosome The function will split the data up into a list of matrices, one per chromosome.

Details

The .cool format is linked a database of Hi-C experiments and allows access to many sets of Hi-C data which can be found at the Index of Coolers ftp://cooler.csail.mit.edu/coolers. Once a .cool file is dumped into a contact matrix in plain text it can be read into R. This function provides a method for converting the .cool matrix into a sparse upper triangular matrix ready to be entered into hic_loess.

Examples

data('cooler')
sparse <- cooler2sparse(cooler)
head(sparse)
#> $chr1
#>          region1   region2   IF
#>     1:         0         0  106
#>     2:         0   1000000  195
#>     3:         0   2000000   59
#>     4:         0   3000000   47
#>     5:         0   4000000   28
#>    ---                         
#> 26026: 247000000 248000000 5758
#> 26027: 247000000 249000000  721
#> 26028: 248000000 248000000 5823
#> 26029: 248000000 249000000 1001
#> 26030: 249000000 249000000  676
#> 
#> $chr10
#>         region1   region2    IF
#>    1:         0         0 15320
#>    2:         0   1000000  4407
#>    3:         0   2000000  1295
#>    4:         0   3000000   953
#>    5:         0   4000000   587
#>   ---                          
#> 8938: 133000000 134000000  2048
#> 8939: 133000000 135000000   262
#> 8940: 134000000 134000000  7008
#> 8941: 134000000 135000000  1094
#> 8942: 135000000 135000000  1338
#> 
#> $chr11
#>         region1   region2    IF
#>    1:         0         0  2115
#>    2:         0   1000000   802
#>    3:         0   2000000   237
#>    4:         0   3000000   110
#>    5:         0   4000000    87
#>   ---                          
#> 8901: 132000000 133000000  9131
#> 8902: 132000000 134000000  1703
#> 8903: 133000000 133000000 21444
#> 8904: 133000000 134000000  4716
#> 8905: 134000000 134000000 18131
#> 
#> $chr12
#>         region1   region2    IF
#>    1:         0         0 11094
#>    2:         0   1000000  6037
#>    3:         0   2000000  1482
#>    4:         0   3000000   646
#>    5:         0   4000000   610
#>   ---                          
#> 8717: 131000000 132000000  3784
#> 8718: 131000000 133000000   442
#> 8719: 132000000 132000000  6241
#> 8720: 132000000 133000000  1286
#> 8721: 133000000 133000000  3694
#> 
#> $chr13
#>         region1   region2   IF
#>    1:  19000000  19000000 2295
#>    2:  19000000  20000000 1435
#>    3:  19000000  21000000  340
#>    4:  19000000  22000000  246
#>    5:  19000000  23000000  208
#>   ---                         
#> 4741: 113000000 114000000 2991
#> 4742: 113000000 115000000  212
#> 4743: 114000000 114000000 6257
#> 4744: 114000000 115000000 1039
#> 4745: 115000000 115000000  699
#> 
#> $chr14
#>         region1   region2   IF
#>    1:  19000000  19000000   33
#>    2:  19000000  20000000  199
#>    3:  19000000  21000000   61
#>    4:  19000000  22000000   26
#>    5:  19000000  23000000   17
#>   ---                         
#> 3981: 105000000 106000000  602
#> 3982: 105000000 107000000  274
#> 3983: 106000000 106000000 2768
#> 3984: 106000000 107000000 2126
#> 3985: 107000000 107000000 1598
#>