Common factor GWAS and TWAS output for nociplastic type pain

file: GSEM_commonFactorGWAS_COPC_6trait_30MAY2023.csv.gz

description: Common factor GWAS output for GenomicSEM analyses of 6 COPC traits (see doi: https://doi.org/10.1101/2023.06.27.23291959)

columns:

SNP = rsID SNP identifier 

CHR = chromosome

BP = base pair position

MAF = minor allele frequency

A1 = effect allele

A2 = other allele

i = index (1 - n SNPs)

lhs = left hand side of equation 

op = equation operator (lavaan syntax)

rhs = right hand side of equation

est = effect size (beta)

se_c = standard error of effect estimate

Z_Estimate = Z value

Pval_Estimate = p value of effect

Q = Q (heterogeneity) value

Q_df = degrees of freedom for Q

Q_pval = Q p value

fail = GSEM fail message if applicable

warning = GSEM warning message if applicable 

Z_smooth = smoothing parameter if applicable 

N_estimate = N estimate 

file: GSEM_commonFactorTWAS_COPC_6trait_30MAY2023.csv.gz

description: Common factor TWAS output for GenomicSEM analyses of 6 COPC traits (see doi: https://doi.org/10.1101/2023.06.27.23291959)

columns:

Gene = ensembl gene ID 

Panel = which model (tissue+gene) i.e. reference weights file

HSQ = gene heritability 

i = index (1 - n gene-tissue models)

lhs = equation left hand side

op = operator (lavaan syntax)

rhs = equation right hand side

est = association estimate (beta)

se_c = standard error of beta

Z_Estimate = Z value 

Pval_Estimate = p value of association test

Q = Q (heterogeneity) value

Q_df = degrees of freedom for Q

Q_pval = p value for Q

fail = GSEM fail message if applicable 

warning = GSEM warning message if applicable 

tissue = tissue

p_bonf_tissue = adjusted p value - bonferroni adjustment within tissue 

p_fdr_tissue = adjusted p value - false discovery rate adjustment within tissue

threshold_bonf_tissue = p value threshold for bonferroni adjustment within tissue 

p_bonf_experiment = adjusted p value - bonferroni adjustment experiment-wide

p_threshold_bonf_experiment = p value threshold (bonferroni, experiment-wide)

Q_bonf_tissue = adjusted p value for Q, bonferroni within-tissue