LDMatrix¶
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class
hail.
LDMatrix
(jldm)[source]¶ Represents a symmetric matrix encoding the Pearson correlation between each pair of variants in the accompanying variant list.
Methods
__init__
matrix
Gets the distributed matrix backing this LD matrix. read
Reads the LD matrix from a file. to_local_matrix
Converts the LD matrix to a local Spark matrix. variant_list
Gets the list of variants. write
Writes the LD matrix to a file. -
matrix
()[source]¶ Gets the distributed matrix backing this LD matrix.
Returns: Matrix of Pearson correlation values. Return type: IndexedRowMatrix
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static
read
(path)[source]¶ Reads the LD matrix from a file.
Examples
Read an LD matrix from a file.
>>> ld_matrix = LDMatrix.read('data/ld_matrix')
Parameters: path (str) – the path from which to read the LD matrix
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to_local_matrix
()[source]¶ Converts the LD matrix to a local Spark matrix.
Caution
Only call this method when the LD matrix is small enough to fit in local memory on the driver.
Returns: Matrix of Pearson correlation values. Return type: Matrix
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