Transfrom a full Hi-C contact matrix to a sparse upper triangular matrix

full2sparse(mat)

Arguments

mat	A matrix. Must have column names equal to the start location for each bin. i.e. for a 6x6 Hi-C matrix where the first region starts at 0 kb and the final region starts at 500KB and the resolution is 100kb, the column names of the matrix should be as follows: colnames(mat) = c(0, 100000, 200000, 300000, 400000, 500000)

Value

A sparse upper triangular matrix.

Examples

m <- matrix(1:100, 10, 10)
colnames(m) <- 1:10
sparse <- full2sparse(m)
sparse
#>     region1 region2  IF
#>  1:       1       1   1
#>  2:       1       2  11
#>  3:       2       2  12
#>  4:       1       3  21
#>  5:       2       3  22
#>  6:       3       3  23
#>  7:       1       4  31
#>  8:       2       4  32
#>  9:       3       4  33
#> 10:       4       4  34
#> 11:       1       5  41
#> 12:       2       5  42
#> 13:       3       5  43
#> 14:       4       5  44
#> 15:       5       5  45
#> 16:       1       6  51
#> 17:       2       6  52
#> 18:       3       6  53
#> 19:       4       6  54
#> 20:       5       6  55
#> 21:       6       6  56
#> 22:       1       7  61
#> 23:       2       7  62
#> 24:       3       7  63
#> 25:       4       7  64
#> 26:       5       7  65
#> 27:       6       7  66
#> 28:       7       7  67
#> 29:       1       8  71
#> 30:       2       8  72
#> 31:       3       8  73
#> 32:       4       8  74
#> 33:       5       8  75
#> 34:       6       8  76
#> 35:       7       8  77
#> 36:       8       8  78
#> 37:       1       9  81
#> 38:       2       9  82
#> 39:       3       9  83
#> 40:       4       9  84
#> 41:       5       9  85
#> 42:       6       9  86
#> 43:       7       9  87
#> 44:       8       9  88
#> 45:       9       9  89
#> 46:       1      10  91
#> 47:       2      10  92
#> 48:       3      10  93
#> 49:       4      10  94
#> 50:       5      10  95
#> 51:       6      10  96
#> 52:       7      10  97
#> 53:       8      10  98
#> 54:       9      10  99
#> 55:      10      10 100
#>     region1 region2  IF