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MetaXcan's Results

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Alvaro Barbeira edited this page Jan 20, 2017 · 2 revisions

The output of metaxcan is a text file that looks like the following:

gene,gene_name,zscore,effect_size,pvalue,VAR_g,pred_perf_R2,pred_perf_p,pred_perf_q,n_snps_used,n_snps_in_cov,n_snps_in_model
ENSG00000150938,CRIM1,-4.19069760413,-0.231471478373,2.78098095601e-05,0.0983344808163,0.13320775358,1.97496173512e-30,7.47907447189e-30,37,37,37
...

Each row will contain information for a successfully processed gene, formatted as:

  • gene: a gene's id: as listed in the Tissue Transcriptome model. Ensemble Id for some, while some others (mainly DGN Whole Blood) provide Genquant's gene name
  • gene_name: gene name as listed by the Transcriptome Model, generally extracted from Genquant
  • zscore: MetaXcan's association result for the gene
  • effect_size: MetaXcan's association effect size for the gene
  • pvalue: P-value of the aforementioned statistic.
  • pred_perf_r2: R2 of tissue model's correlation to gene's measured transcriptome (prediction performance)
  • pred_perf_pval: pval of tissue model's correlation to gene's measured transcriptome (prediction performance)
  • pred_perf_qval: qval of tissue model's correlation to gene's measured transcriptome (prediction performance)
  • n_snps_used: number of snps from GWAS that got used in MetaXcan analysis
  • n_snps_in_cov: number of snps in the covariance matrix
  • n_snps_in_model: number of snps in the model
  • var_g: variance of the gene expression, calculated as W' * G * W (where W is the vector of SNP weights in a gene's model, W' is its transpose, and G is the covariance matrix)
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