doc/OutputFiles.md

In n-mounier/bGWAS: Bayesian Genome-Wide Association Study

Output files

If save_files=TRUE, several files are created in the folder ./<name>/.

Description

The output files created are: - .log - report containing everything that has been printed during the bGWAS analysis (is verbose=TRUE)

• PriorGWASs.tsv : contains information about all prior GWASs (general info + status (used/removed) + MR coefficients):

  File : prior GWAS file name Name : prior GWAS name Trait : phenotypical category (both Systolic and Diastiolic Blood Pressure are part of "Blood Pressure" for example) status : has the file been used to create the prior? (can be "USED", "Excluded by user", "Excluded for MR: removale reason") uni_estimate : causal effect estimate from uniivariable MR uni_std_error : causal effect standard error from uniivariable MR uni_T : T-statistic from uniivariable MR uni_P : p-value from uniivariable MR uni_adj_Rsquared : adjusted R squared from uniivariable MR uni_Rsquared : R squared from uniivariable MR multi_estimate : causal effect estimate from multivariable MR multi_std_error : causal effect standard error from multivariable MR multi_T : T-statistic from multivariable MR multi_P: p-value estimate from multivariable MR

• CoefficientsByChromosome.csv : contains the MR estimates when masking the focal chromosome (22 coefficients / prior GWASs used for prior estimation)

  study : everything that is printed during a bGWAS analysis (if verbose=TRUE) estimate : causal effect estimate from multivariable MR (masking one chromosome) std_error : causal effect standard error from multivariable MR (masking one chromosome) T : T-statistics from multivariable MR (masking one chromosome) P : p-value from multivariable MR (masking one chromosome) chrm : chromosome masked

• PriorBFp.csv : contains BF and p-values, prior, posterior and direct effects estimates for all SNPs

  chrm_UK10K : chromosome (obtained from UK10K data) pos_UK10K : position (obtained from UK10K data) rsid : rs number alt : alternative (effect) allele ref : reference allele beta : observed effect size se : observed standard error z_obs : observed Z-score mu_prior_estimate : prior effect estimate (z-score scale) mu_prior_std_error : prior effect standard error (z-score scale) mu_posterior_estimate : posterior effect estimate (z-score scale) mu_posterior_std_error : posterior effect standard error (z-score scale) z_posterior : posterior Z-score mu_direct_estimate : direct effect estimate (z-score scale) mu_direct_std_error : direct effect standard error (z-score scale) z_direct : direct Z-score beta_prior_estimate : prior effect estimate (beta scale) beta_prior_std_error : prior effect standard error (beta scale) beta_posterior_estimate : posterior effect estimate (beta scale) beta_posterior_std_error : posterior standard error estimate (beta scale) beta_direct_estimate : direct effect estimate (beta scale) beta_direct_std_error : direct effect standard error (beta scale) BF : Bayes Factor BF_p/BF_fdr : Bayes Factor p-value / fdr p_posterior : posterior effect p-value / fdr p_direct : direct effect p-value / fdr
  CRR : corrected to raw ratio (ratio between direct effect and observed effect)

SignificantSNPs.csv : contains BF and p-values, prior, posterior and direct effects estimates for a subset of significant SNPs (subset of PriorBFp.csv)

n-mounier/bGWAS documentation built on Oct. 11, 2023, 1:39 a.m.