pandas_plink.read_rel¶
- pandas_plink.read_rel(filepath, id_filepath=None)[source]¶
Read PLINK realized relationship matrix files [b].
It supports plain text, binary, and compressed files. The usual file extensions for those types are .rel, .rel.bin, and .rel.zst, respectively.
Example
>>> from os.path import join >>> from pandas_plink import read_rel >>> from pandas_plink import get_data_folder >>> filepath = join(get_data_folder(), "rel-bin", "plink2.rel.bin") >>> id_filepath = join(get_data_folder(), "rel-bin", "plink2.rel.id") >>> K = read_rel(filepath, id_filepath) >>> print(K) <xarray.DataArray (sample_0: 10, sample_1: 10)> array([[ 0.89, 0.23, -0.19, -0.01, -0.14, 0.29, 0.27, -0.23, -0.10, -0.21], [ 0.23, 1.08, -0.45, 0.19, -0.19, 0.17, 0.41, -0.01, -0.13, -0.13], [-0.19, -0.45, 1.18, -0.04, -0.15, -0.20, -0.31, -0.04, 0.30, -0.01], [-0.01, 0.19, -0.04, 0.90, -0.07, 0.01, 0.06, -0.19, -0.09, 0.17], [-0.14, -0.19, -0.15, -0.07, 1.18, 0.09, -0.03, 0.10, 0.22, 0.17], [ 0.29, 0.17, -0.20, 0.01, 0.09, 0.96, 0.07, -0.04, -0.09, -0.23], [ 0.27, 0.41, -0.31, 0.06, -0.03, 0.07, 0.71, -0.10, -0.09, -0.06], [-0.23, -0.01, -0.04, -0.19, 0.10, -0.04, -0.10, 1.42, -0.30, -0.07], [-0.10, -0.13, 0.30, -0.09, 0.22, -0.09, -0.09, -0.30, 0.91, -0.02], [-0.21, -0.13, -0.01, 0.17, 0.17, -0.23, -0.06, -0.07, -0.02, 0.91]]) Coordinates: * sample_0 (sample_0) object 'HG00419' 'HG00650' ... 'NA20508' 'NA20753' * sample_1 (sample_1) object 'HG00419' 'HG00650' ... 'NA20508' 'NA20753' fid (sample_1) object 'HG00419' 'HG00650' ... 'NA20508' 'NA20753' iid (sample_1) object 'HG00419' 'HG00650' ... 'NA20508' 'NA20753'
- Parameters
- Returns
rel – Realized relationship matrix.
- Return type
References
- b
Read PLINK realized relationship matrix files. https://www.cog-genomics.org/plink/2.0/distance