Analysis is DNAm associations with SES in the PAWS cohort
DNAm data is located at GSE94734
| Script | Action | Input | Output |
|---|---|---|---|
| SNP_final_report_Loading_annotated.rmd | Pulls the files from genome studio; Runs quality control to remove bad samples; Runs quality controls to remove bad probes; Does and initial PCA to pull out genetic clusters (but PLINK is the more comprehensive method); Builds ped and map files for PLINK analysis | PAWS_psychchip_DNAReport.csv PAWS_psychchip_FinalReport_B_allele_freq.txt | PAWS_snps_GCScore.RData Quality_control_removed_SNPs.RData PAWS_snps_filtered.RData PAWS_snps_Ballelefreq.RData |
| Normalization.Rmd | Pull files from genome studio; Match PsychChip and 450K based on 15 SNPs; Probe Filter (forgot polymorphic CpGs so did it later); BMIQ normalization | PAWS.all-alldata.txt PAWS-GdatasetforKoborlabJuly2014-ID_ordered.csv PAWS.all-samplefile.txt | PAWS_sampFiltered_prbFilter_BMIQ.RData PAWS_sample_info_with_replicates.csv |
| PLINK_Data_Prep_annotated.Rmd | Make ped and map files for PLINK | PAWS_snps_filtered.RData PAWS-GdatasetforKoborlabJuly2014-ID_ordered.csv | PAWS_snps_filtered_MAP.txt PAWS_snps_filtered_ped.txt |
| GEO_Data_blood_w_age.Rmd | Pulls blood form GEO with similar age range | GEO | GEO_blood_age_samples.RData GEO_PAWS_aged_matched_whole_blood.RData GSE53191.RData GSE50222.RData |
| Post_Normalization_QC.Rmd | Sorts our the mets data; T-cell and blood contamination testing; Heat scree plots; Meta data correlation; covariate testing for model building; ComBat; Replicate RMSE | PAWS_Beta_norm_filtered.RData PAWS_sample_info_with_replicates.csv PAWS-GdatasetforKoborlabJan2015-.csv 2014-09-03_pawsSampleSheet_all.csv GSE53191.RData GSE50222.RData GEO_PAWS_aged_matched_whole_blood.RData | PAWS_meta_sentrix_genetic_clusters.RData combat_PAWS_Beta_norep.RData |
| Regression_deinc2dep.R | Runs LME on mvalues for income per dependent | combat_PAWS_Beta_norep.RData PAWS_meta_sentrix_genetic_clusters.RData SNPCpG.RData | deinc2dep_PAWS_hits_Mval.RData deinc2dep_PAWS_hits_Mval.RData |
| Regression_FADV_6.R | Runs LME on mvalues for adversity | combat_PAWS_Beta_norep.RData PAWS_meta_sentrix_genetic_clusters.RData SNPCpG.RData | Likelihood_Ratio_Test_lmer_FADV_6_PAWS_Mval_genetic_cluster_and_twin_fixed_allFactors.RData FADV_6_PAWS_hits_Mval.RData |
| Regression_HGHEDLV2.R | Runs LME on mvalues for highest education level | combat_PAWS_Beta_norep.RData PAWS_meta_sentrix_genetic_clusters.RData SNPCpG.RData | Likelihood_Ratio_Test_lmer_HGHEDLV2_PAWS_Mval_genetic_cluster_and_twin_fixed_allFactors.RData HGHEDLV2_PAWS_hits_Mval.RData |
| Genetic_cluster_anova.R | Collect CpG at which methylation associates with genetic ancestry for removal from main hit lists | combat_PAWS_Beta_norep.RData PAWS_meta_sentrix_genetic_clusters.RData | Genetic_cluster_hits.RData |
| Overlap_regression interpretation.R | Generates numbers for hit count tables; Makes CpG-Gene association tables; Tests overlap between income, adversity and education at gene level; Plot individual CpGs; Island Gene body enrichment | combat_PAWS_Beta_norep.RData PAWS_meta_sentrix_genetic_clusters.RData SNPCpG.RData Genetic_cluster_hits.RData FADV_6_PAWS_hits_Mval.RData HGHEDLV2_PAWS_hits_Mval.RData deinc2dep_PAWS_hits_Mval.RData Gene_enrichment_functions.R | Gene/CpG tables and figures no major R objects |
| Pyro_site_selection_and_confirmation.R | Selectionof CpGs with big delta beta for Pyro | All the things above; csv files from the pyro for each sample | Plots |
| Script | Action | Input | Output |
|---|---|---|---|
| sensitivity_analysis_blood_gender.R | Run original linear models but with coraviates for gender and blood contmination | combat_PAWS_Beta_norep.RData PAWS_meta_sentrix_genetic_clusters.RData SNPCpG.RData | plots and p values |