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TWAS weights released on Synapse use the legacy list layout, which pecotmr 0.8.x does not read. This adds a protocol-level conversion layer, as agreed, rather than a backwards-compatibility loader in pecotmr. - twas_weights_conversion.R: convert legacy weight RDS (univariate and multicontext) into one pecotmr TwasWeights per gene. Weights and CV metrics are copied unchanged; carries traitPos (gene TSS) for cTWAS block placement; writes the xqtl_meta row and the context -> data type rows. - twas_ctwas.ipynb: new optional twas_weights_conversion workflow (skip it for weights already in TwasWeights format), with Input/Output/MWE docs and the Overview updated; MWE commands now use the converted example tables. - ctwas_1: --gwas_study now selects the GWAS (cTWAS takes one per LD block) and the run fails early if several remain; new --ctwas_method (weights with several methods and no ensemble); pass the chromosome's genotype prefix as --ld-sketch so ctwasPipeline sees a real LD file rather than a "<chrom-meta>" placeholder. - ctwas_assemble.R: drop study elements and LD blocks with no GWAS variants (they carry no genome build and broke combineGwasSumStats). Tested: conversion is exact for eQTL, pQTL and sQTL weights (weights compared element by element); TWAS runs on converted weights for 8 studies in the APOE region; cTWAS assemble passes. cTWAS parameter estimation and fine-mapping are not yet tested. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Csueazw8VDi9a3mhLvgjQg
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TWAS weights released on Synapse use the legacy list layout, which pecotmr 0.8.2 does not read. This adds a protocol-level conversion layer, as agreed, rather than a backwards-compatibility loader in pecotmr.
twas_weights_conversion.R: convert legacy weight RDS (univariate and multicontext) into one pecotmr TwasWeights per gene. Weights and CV metrics are copied unchanged; carries traitPos (gene TSS) for cTWAS block placement; writes the xqtl_meta row and the context -> data type rows.twas_ctwas.ipynb: new optional twas_weights_conversion workflow (skip it for weights already in TwasWeights format), with Input/Output/MWE docs and the Overview updated; MWE commands now use the converted example tables.ctwas_1: --gwas_study now selects the GWAS (cTWAS takes one per LD block) and the run fails early if several remain; new --ctwas_method (weights with several methods and no ensemble); pass the chromosome's genotype prefix as --ld-sketch so ctwasPipeline sees a real LD file rather than a "" placeholder.ctwas_assemble.R: drop study elements and LD blocks with no GWAS variants (they carry no genome build and broke combineGwasSumStats).Tested: conversion is exact for eQTL, pQTL and sQTL weights (weights compared element by element); TWAS runs on converted weights for 8 studies in the APOE region; cTWAS assemble passes. cTWAS parameter estimation and fine-mapping are not yet tested.