Source code of the manuscript "The value of genetic data from 665 460 individuals in predicting anemia and suitability to donate blood".
| File |
Description |
| pipeline-phewas-30k.svg |
Description of the R5 pipeline |
Exploratory analysis prior to running GWAS with Saige
| File |
Description |
| anemia_metaresults_analysis.Rmd Explore the results of the FG+UKBB meta-analysis of IDA |
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| compare_progesa_and_finngen.Rmd |
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| compare_finngen_and_1kg.Rmd |
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| explore_deferral_dataframe.Rmd |
Explore the contents of the deferral dataframe |
| explore_haitat_dataframes.Rmd |
Explore the contents of the defects dataframe |
| venn_diagram.Rmd |
Simple test of using the RVenn package |
| compute_phenotypes.Rmd |
Compute the phenotypes for the GWAS |
| File |
Description |
| gwas_pipeline.sh |
Runs the full Saige pipeline |
| common.R |
Common functions an dataframe used in many places |
| common.sh |
Contains the paths of the 1KG, FinnGen and result files |
| epouta-common.sh |
Contains the paths on the ePouta environment |
| do-pca-and-grm-data.sh |
Pipeline for PCA and GRM |
| clean-data-for-pca.sh |
Perform quality control for PCA and GRM |
| find_duplicates.R |
Create a set of duplicate variants |
| find_outliers.R |
Find and visualize the PCA outliers |
| post-pca.sh |
Pipeline that removes outliers, does IBD analysis and performs PCA for the second time |
| ibd_analysis.R |
Perform the Independence by Descent analysis |
| find_bad_relatives.R |
Create a set of individuals to be removed, so that no too close relatives exists |
| convert-to-bed.sh |
Convert VCF files to BED format |
| clean-data.sh |
Perform quality control for GWAS |
| remove-duplicates.sh |
Remove duplicate variants |
| prepare_saige_input.R |
Combine that PCA, covariate and phenotype dataframes |
| process_saige_output.R |
Create the Manhattan and QQ plots after Saige has run |
| File |
Description |
| run.sh |
Runs both steps of Saige |
| step1_fitNULLGLMM.R |
Saige step1 |
| step2_SPAtests.R |
Saige step2 |
Analysis done after Saige pipeline
| File |
Description |
| anemia_logistic_and_cox.Rmd |
Fit logistic regression and Cox models for iron deficiency anemia |
| deferral_logistic_and_cox.Rmd |
Fit logistic regression and Cox models for Hb deferral |
| pca-on-map-of-finland.Rmd |
Plot the PCA results and outliers. |
| FIN_adm4.sf.rds |
Data of Finnish geographical map |
| prepare-for-vep.sh |
Convert Saige summary stats to a form that VEP requires |
| get_coefficients.R |
Extract the coefficients of the Saige null models |
| get-exclusions2.sh |
Extract the data exclusion counts from the PLINK log files |
| get-exclusions.sh |
Another version of the above |
| create_excel_functions |
R Helper functions |
| create_excel.R |
Create an annotated Excel files of the GWAS results |
| create_anemia_and_deferral_article_results.Rmd |
Create tables and figures for the anemia article |