Replace ctwas_ld_loader with ld_loader LD_info mode#463
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Add LD_info mode to ld_loader(): accepts a data.frame with LD_file (and optionally SNP_file) columns, loading .cor.xz blocks on demand via process_LD_matrix(). This is the fourth mode alongside R_list, X_list, and ld_meta_path. Remove ctwas_ld_loader() entirely. Its functionality is now covered by: loader <- ld_loader(LD_info = get_ctwas_meta_data(...)$LD_info) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
process_LD_matrix() now auto-detects variant file format: - .bim (PLINK1): 6 or 9 column tab-separated, no header - .pvar/.pvar.zst (PLINK2): header starting with #CHROM, read via existing read_pvar_text() When snp_file_path is NULL, tries .bim, .pvar, .pvar.zst in order. The ld_loader LD_info mode now passes NULL to let auto-detection work instead of hardcoding .bim. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
The LD_info mode now auto-detects and handles: 1. Pre-computed .cor.xz + .bim/.pvar (custom block format) 2. PLINK1 prefix (.bed/.bim/.fam) - LD computed via compute_LD() 3. PLINK2 prefix (.pgen/.pvar/.psam) - LD computed via compute_LD() Format is detected by checking which files exist at the LD_file path using has_plink2_files() and has_plink1_files(). Falls back to process_LD_matrix() for .cor.xz blocks. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Summary
LD_infomode told_loader(): accepts a data.frame withLD_file(and optionallySNP_file) columns, loading.cor.xzblocks on demand viaprocess_LD_matrix()ctwas_ld_loader()entirely — its functionality is now covered byld_loader(LD_info = get_ctwas_meta_data(...)$LD_info)ld_loader()now has 4 unified modes:R_list,X_list,ld_meta_path+regions,LD_infoUsage
Test plan
R CMD checkpassesctwas_ld_loaderdirectly)🤖 Generated with Claude Code