KinshipMatrix¶
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class
hail.genetics.
KinshipMatrix
(jkm)[source]¶ Represents a symmetric matrix encoding the relatedness of each pair of samples in the accompanying sample list.
We plan to remove this class in Hail 0.2 while maintaining its functionality.
The output formats are consistent with PLINK formats as created by the make-rel and make-grm commands and used by GCTA.
Attributes
key_schema
Returns the signature of the key indexing this matrix. Methods
__init__
Initialize self. export_gcta_grm
Export kinship matrix as . export_gcta_grm_bin
Export kinship matrix as . export_id_file
Export samples as . export_rel
Export kinship matrix as . export_tsv
Export kinship matrix to tab-delimited text file with sample list as header. matrix
Gets the matrix backing this kinship matrix. sample_list
Gets the list of samples. -
export_gcta_grm
(output)[source]¶ Export kinship matrix as .grm file. See PLINK formats.
Parameters: output (str) – File path for output.
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export_gcta_grm_bin
(output, opt_n_file=None)[source]¶ Export kinship matrix as .grm.bin file or as .grm.N.bin file, depending on whether an N file is specified. See PLINK formats.
Parameters: - output (str) – File path for output.
- opt_n_file (str or None) – The file path to the N file.
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export_id_file
(output)[source]¶ Export samples as .id file. See PLINK formats.
Parameters: output (str) – File path for output.
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export_rel
(output)[source]¶ Export kinship matrix as .rel file. See PLINK formats.
Parameters: output (str) – File path for output.
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export_tsv
(output)[source]¶ Export kinship matrix to tab-delimited text file with sample list as header.
Parameters: output (str) – File path for output.
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matrix
()[source]¶ Gets the matrix backing this kinship matrix.
Returns: MatrixTable of kinship values. Return type: IndexedRowMatrix
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