Read in LD (linkage disequilibrium) matrix from a TSV file.

The LD matrix should be a symmetric correlation matrix where rows and columns represent SNPs. The file should be tab-separated with SNP IDs as column headers. Rows with infinite or NaN values are automatically removed.

Parameters:

path: str¶

The path to the LD matrix file (tab-separated, .tsv format).

Returns:

LD correlation matrix with SNP IDs as index and columns.

Return type:

pd.DataFrame

Example

Read LD matrix for fine-mapping:

from sushie.io import read_ld

# Read LD matrix
ld = read_ld("path/to/ld_matrix.tsv")
print(ld.shape)  # Should be (n_snps, n_snps)