trackc.tl.extractContactRegions#

trackc.tl.extractContactRegions(clr: Cooler | str, balance: bool = False, row_regions: Sequence[str] | str | None = None, col_regions: Sequence[str] | str | None = None) → RegionsCmat[source]#

Extract a set of regions matrix from the cool format Hi-C matrix.

The extracted matrix will splice intra and inter region interaction according to the given order and direction of the regions.

Parameters:

  • clr (cooler.Cooler | str) –

    cool format Hi-C matrix (open2c/cooler) or cool file path

    cooler.Cooler e.g. GM12878=cooler.Cooler(‘./GM12878.chr18.mcool::/resolutions/50000’)

    str e.g. ‘GM12878.chr18.mcool::/resolutions/50000’ or ‘GM12878.chr18.cool’

  • balance (bool) – The 'balance' parameters of coolMat.matrix(balance=False).fetch('chr6:119940450-123940450')

  • row_regions (str | str list | None.) – The subset matrix row genome regions. e.g. "chr6:1000000-2000000", e.g. ["chr6:1000000-2000000", "chr3:5000000-4000000", "chr5"] The start can be larger than the end (e.g. "chr6:2000000-1000000"), which means you want to get the reverse region contact matrix

  • col_regions (str | str list | None.) – The subset matrix col genome regions, default is None, which means the sample region as row_regions

  • Returns –

  • -------- –

    RegionsCmat

    row_regions and col_regions contact matrix object

Example

>>> import trackc as tc
>>> import cooler

>>> mat1 = tc.tl.extractContactRegions(clr='GM12878.chr18.mcool::/resolutions/50000', row_regions="18:45000000-78077248")
>>> GM12878 = cooler.Cooler('./GM12878.chr18.mcool::/resolutions/50000')
>>> mat2 = tc.tl.extractContactRegions(clr=GM12878, row_regions=["18:61140000-63630000", "18:74030000-77560000"], col_regions="18:47340000-50370000")
>>> print(mat2.cmap.shape)
>>> print(mat2.row_regions)
>>> print(mat2.col_regions)