Additional file 11 of Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression

Additional file 11: Table S3. Results for SNP–CpG association analysis based on R limma models. Tables for screening and recall are provided separately. Limma models were run independently for every SNP site for all available CpG sites; only statistically significant results are shown. Adjusted p values were calculated using the false discovery rate method for every SNP separately. Adjusted p values were further adjusted by the number of SNP sites tested. Additionally, moderated t values from limma were adjusted for genomic inflation and bias with the R package bacon. Similar statistics as for limma t values were calculated for bacon-adjusted t values. Cumulated positions for CpGs were calculated based on the data from ( https://www.ncbi.nlm.nih.gov/grc/human/data?asm=GRCh37 ). Associated genes and coordinates for CpGs were obtained from Illumina annotation files for a corresponding array. Column names state the following: Gene, a gene associated with an SNP; SNP, investigated SNP; SNP coords, coordinates of SNP; CpG; associated CpG site; CpG chrom., a chromosome of a CpG; CpG pos., coordinates of a CpG (for the current chromosome); CpG cumul. Pos., the cumulative position of a CpG; CpG gene, a gene associated with a CpG; logFC, estimate of the log2-fold-change corresponding to the effect; AveExpr, average log2 value for the probe over all arrays and channels; t, moderated t-statistic; P.Value, raw p value; adj.P.Value, FDR-adjusted p value with no correction for the number of SNPs and inflation/bias; B, log-odds that the site is differentially methylated; adj.P.Val.SNP, limma FDR-adjusted p value corrected for the number of SNPs; Inflation.Bacon, inflation factor calculated in bacon; Bias.Bacon, bias of estimations; T.Bacon, corrected moderated T statistics; P.val.Bacon, p value after correction for inflation and bias; Adj.P.Val.Bacon, FDR-adjusted p value after correction for inflation and bias; adj.P.Val.SNP.Bacon, FDR-adjusted p value corrected for the number of SNPs, inflation, and bias. Abbreviations: SNP, single nucleotide polymorphism; FDR, false discovery rate.