Spredixcan Tools

Configuration File: spredixcan_tools.json Tool Type: Local Tools Count: 1

This page contains all tools defined in the spredixcan_tools.json configuration file.

Available Tools

SPrediXcan_associate (Type: SPrediXcanTool)

Summary-based transcriptome-wide association (S-PrediXcan, Barbeira 2018): test a gene for trait …

SPrediXcan_associate tool specification

Tool Information:

  • Name: SPrediXcan_associate

  • Type: SPrediXcanTool

  • Description: Summary-based transcriptome-wide association (S-PrediXcan, Barbeira 2018): test a gene for trait association by combining its eQTL prediction weights with GWAS per-SNP z-scores. Returns the gene TWAS z-score and p-value. Pure-compute (no individual-level data, no LD panel needed when SNPs are independent/LD-pruned; optionally supply a SNP covariance matrix). Pairs with eQTL_get_associations + GWAS summary tools.

Parameters:

  • weight (array) (required) Per-SNP eQTL prediction weights for the gene (same SNP order as gwas_z).

  • gwas_z (array) (required) Per-SNP GWAS z-scores (beta/se), same SNP order.

  • snp_sd ([‘array’, ‘null’]) (optional) Per-SNP standard deviation (~sqrt(2*MAF*(1-MAF))); default 1.0 (standardized).

  • covariance ([‘array’, ‘null’]) (optional) Optional SNP covariance matrix (n x n, same SNP order). If omitted, SNPs are assumed independent.

  • snp ([‘array’, ‘null’]) (optional) Optional SNP identifiers (same order), for reference.

Example Usage:

query = {
    "name": "SPrediXcan_associate",
    "arguments": {
        "weight": ["item1", "item2"],
        "gwas_z": ["item1", "item2"]
    }
}
result = tu.run(query)