KinshipMatrix

class hail.KinshipMatrix(jkm)

Represents a symmetric matrix encoding the relatedness of each pair of samples in the accompanying sample list.

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__
export_gcta_grm	Export kinship matrix as .grm file.
export_gcta_grm_bin	Export kinship matrix as .grm.bin file or as .grm.N.bin file, depending on whether an N file is specified.
export_id_file	Export samples as .id file.
export_rel	Export kinship matrix as .rel file.
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)

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)

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)

Export samples as .id file. See PLINK formats.

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

export_rel(output)

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

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

export_tsv(output)

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:Type

matrix()

Gets the matrix backing this kinship matrix.

Returns:Matrix of kinship values. Return type:IndexedRowMatrix

sample_list()

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