This repository contains code used for the tutorial (IGES_CrossBioBank_PracticalTutorial.Rmd) as well as scripts used to create the data and test analyses used in the tutorial (scripts/).
- All the source data are publicly available;
- All the source code are open-access;
- All the analysis results are reproducible.
The packages used in the tutorial include:
install.packages("devtools")
install.packages("Matrix")
install.packages("BiocManager")
install.packages('restfulr')
install.packages('logistf')
install.packages('GMMAT')
install.packages("remotes")
install.packages("dplyr")
BiocManager::install('S4Vectors')
BiocManager::install('gdsfmt')
BiocManager::install('SeqArray')
BiocManager::install('SeqVarTools')
BiocManager::install('GENESIS')
BiocManager::install('GenomicFeatures')
BiocManager::install('TxDb.Hsapiens.UCSC.hg38.knownGene')
devtools::install_github('xihaoli/STAAR')
devtools::install_github('zilinli1988/SCANG')
devtools::install_github('xihaoli/MultiSTAAR',ref='main')
devtools::install_github('xihaoli/STAARpipeline',ref='main')
devtools::install_github('xihaoli/STAARpipelineSummary',ref='main')
devtools::install_github('xihaoli/MetaSTAAR',ref='main')
devtools::install_github("li-lab-genetics/MetaSTAARlite",ref="main")
remotes::install_github("privefl/bigsnpr")The data used for this tutorial is available at https://dataverse.harvard.edu/api/access/datafile/11945376.
This contains a tar.gz file with data used in the IGES 2025 Cross Biobank Practical Tutorial. The vcf used in this tutorial to create common variants and agds files is from 1000G (https://doi.org/10.1016/j.cell.2022.08.004) and downloadable at https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/. Unrelated individuals were identified using the panel downloadable from https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/. All other files were created or simulated using the code in the scripts/ folder.
download.file(url = "https://dataverse.harvard.edu/api/access/datafile/11945376",
destfile = "")Please see the IGES Cross Biobank Practical Tutorial for a step-by-step tutorial of the 2025 IGES Education Workshop in Cologne, Germany.
> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS 15.6.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] MetaSTAARlite_0.9.7 bigsnpr_1.12.21 bigstatsr_1.6.2 STAARpipeline_0.9.7.2
loaded via a namespace (and not attached):
[1] rstudioapi_0.17.1 jsonlite_1.8.9
[3] shape_1.4.6.1 magrittr_2.0.3
[5] jomo_2.7-6 GenomicFeatures_1.58.0
[7] logistf_1.26.0 nloptr_2.1.1
[9] rmarkdown_2.29 BiocIO_1.16.0
[11] zlibbioc_1.52.0 vctrs_0.6.5
[13] memoise_2.0.1 minqa_1.2.8
[15] Rsamtools_2.22.0 SNPRelate_1.40.0
[17] RCurl_1.98-1.16 quantsmooth_1.72.0
[19] CompQuadForm_1.4.3 htmltools_0.5.8.1
[21] S4Arrays_1.6.0 curl_6.0.1
[23] broom_1.0.7 SparseArray_1.6.0
[25] mitml_0.4-5 desc_1.4.3
[27] sandwich_3.1-1 zoo_1.8-12
[29] cachem_1.1.0 GenomicAlignments_1.42.0
[31] lifecycle_1.0.4 iterators_1.0.14
[33] pkgconfig_2.0.3 Matrix_1.7-1
[35] R6_2.6.1 fastmap_1.2.0
[37] GenomeInfoDbData_1.2.13 MatrixGenerics_1.18.0
[39] digest_0.6.37 colorspace_2.1-1
[41] SCANG_1.0.4 GWASTools_1.52.0
[43] AnnotationDbi_1.68.0 S4Vectors_0.44.0
[45] ps_1.8.1 rmio_0.4.0
[47] GenomicRanges_1.58.0 RSQLite_2.3.9
[49] httr_1.4.7 abind_1.4-8
[51] mgcv_1.9-1 compiler_4.4.1
[53] rngtools_1.5.2 remotes_2.5.0
[55] doParallel_1.0.17 bit64_4.5.2
[57] backports_1.5.0 BiocParallel_1.40.0
[59] DBI_1.2.3 MultiSTAAR_0.9.7.1
[61] bigassertr_0.1.7 pkgbuild_1.4.5
[63] pan_1.9 MASS_7.3-61
[65] quantreg_5.99.1 STAAR_0.9.7.2
[67] DelayedArray_0.32.0 rjson_0.2.23
[69] DNAcopy_1.80.0 gdsfmt_1.42.0
[71] tools_4.4.1 lmtest_0.9-40
[73] GMMAT_1.4.2 nnet_7.3-19
[75] glue_1.8.0 quadprog_1.5-8
[77] restfulr_0.0.15 callr_3.7.6
[79] nlme_3.1-166 bigparallelr_0.3.2
[81] grid_4.4.1 GENESIS_2.36.0
[83] generics_0.1.4 operator.tools_1.6.3
[85] gtable_0.3.6 bigsparser_0.7.3
[87] flock_0.7 formula.tools_1.7.1
[89] tidyr_1.3.1 data.table_1.16.4
[91] XVector_0.46.0 BiocGenerics_0.52.0
[93] GWASExactHW_1.2 foreach_1.5.2
[95] pillar_1.11.0 splines_4.4.1
[97] dplyr_1.1.4 lattice_0.22-6
[99] survival_3.7-0 rtracklayer_1.66.0
[101] bit_4.5.0.1 SparseM_1.84-2
[103] tidyselect_1.2.1 SeqVarTools_1.44.0
[105] kinship2_1.9.6.1 Biostrings_2.74.0
[107] knitr_1.49 IRanges_2.40.1
[109] SummarizedExperiment_1.36.0 stats4_4.4.1
[111] xfun_0.49 expm_1.0-0
[113] Biobase_2.66.0 matrixStats_1.4.1
[115] UCSC.utils_1.2.0 yaml_2.3.10
[117] boot_1.3-31 TxDb.Hsapiens.UCSC.hg38.knownGene_3.20.0
[119] evaluate_1.0.1 codetools_0.2-20
[121] tibble_3.3.0 cli_3.6.5
[123] rpart_4.1.23 munsell_0.5.1
[125] processx_3.8.4 MetaSTAAR_0.9.6.3
[127] Rcpp_1.1.0 GenomeInfoDb_1.42.1
[129] png_0.1-8 XML_3.99-0.17
[131] parallel_4.4.1 MatrixModels_0.5-3
[133] ggplot2_3.5.2 blob_1.2.4
[135] STAARpipelineSummary_0.9.7.1 doRNG_1.8.6.2
[137] bitops_1.0-9 lme4_1.1-35.5
[139] glmnet_4.1-8 SeqArray_1.46.0
[141] scales_1.3.0 purrr_1.0.2
[143] crayon_1.5.3 rlang_1.1.6
[145] cowplot_1.2.0 KEGGREST_1.46.0
[147] mice_3.17.0This software is licensed under GPLv3.
