KinshipMatrix

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.
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.
export_id_file(output)[source]

Export samples as .id file. See PLINK formats.

Parameters:output (str) – File path for output.
export_rel(output)[source]

Export kinship matrix as .rel file. See PLINK formats.

Parameters:output (str) – File path for output.
export_tsv(output)[source]

Export kinship matrix to tab-delimited text file with sample list as header.

Parameters:output (str) – File path for output.
key_schema

Returns the signature of the key indexing this matrix.

Return type:HailType
matrix()[source]

Gets the matrix backing this kinship matrix.

Returns:MatrixTable of kinship values.
Return type:IndexedRowMatrix
sample_list()[source]

Gets the list of samples. The (i, j) entry of the matrix encodes the relatedness of the ith and jth samples.

Returns:List of samples.
Return type:list of str