raiss.ld_matrix

Function set to compute LD correlation from a reference panel in predefined Region

LD matrix are then transformed to the pandas sparse format

Functions

generate_genome_matrices(region_files, ...)	go through region files and compute LD matrix for each transform and save the results in a pandas sparse dataframe
generate_sparse_matrix(plink_ld, ref_chr_df)	Extract correlation matrix from the plink correlation file generated by ld_matrix.launch_plink_ld read plink results create a sparse dataframe LD-matrix then save it to a zipped pickle
launch_plink_ld(startpos, endpos, chr, ...)	launch plink linkage desiquilibrium correlation and save the ouput
load_plink_ld(plink_ld, ref_chr_df)
load_sparse_matrix(path_sparse_LD, ref_chr_df)	Load matrix from LD matrix from scipy sparse file