Repository contains reproducible analyses for the paper: Jedynak et al., 2023.
Analyses depend on R (>= 4.3.0).
Code used to produce the files is found in the corresponding file: jedynak_prenatal_2023.Rmd (executable file).
This analysis was performed under Windows 11 x64 (build 22621) using:
- R 4.3.1 (2023-06-16 ucrt)
- renv 1.0.0 dependency management package
All packages used in the analyses are saved in the renv/library/R-4.3/x86_64-w64-mingw32 folder at the version used to produce these results, under control of the renv package manager. Re-running the analysis requires execution of renv::restore() which will upgrade/ downgrade user's packages to the versions used in the present study. This operation will modify the packages only locally (for the project), so it will not affect user's package library. All "in-house" packages are available in the R/ folder.
Re-running the analysis requires an additional data/raw_data folder that is not shared here. These data can only be provided upon request and after approval by the SEPAGES consortium (contact: Sarah Lyon-Caen). Running the script: jedynak_prenatal_2023.Rmd will allow to fully reproduce the analyses, figures and tables.
Analysis input data-files are not made available as they contain sensitive information. The analysis input data files would be:
data_sepages_211022.sas7bdat= covariates data, including potential confounders, n = 484phenols_phthalates_pregnancy_mr_2020-03-26_448.csv= phenols exposure data, n = 479bmiq_processed.RDS= methylation data (no replicates, 814,481 CpGs, not filtered, normalized using BMIQ method), n = 395SEPAGES_SampleSheet_nodup_20211208.csv= DNA methylation measurement technical factors (batch, plate, chip), n = 395SEPAGES_CC.planet_rpc.csv= placental cell mix proportionsdata_nsample_230314.Rdata= data on number of urine samples per pool
Additional file EWAS_rep_nl_FDR.RDS is not available in the repo due to its large size.
This folder contains all the in-house functions and packages used for the analyses.
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)
Matrix products: default
locale:
[1] LC_COLLATE=English_Europe.utf8 LC_CTYPE=English_Europe.utf8
[3] LC_MONETARY=English_Europe.utf8 LC_NUMERIC=C
[5] LC_TIME=English_Europe.utf8
time zone: Europe/Madrid
tzcode source: internal
attached base packages:
[1] parallel stats4 stats graphics grDevices datasets utils
[8] methods base
other attached packages:
[1] lubridate_1.9.2
[2] forcats_1.0.0
[3] stringr_1.5.0
[4] dplyr_1.1.2
[5] purrr_1.0.1
[6] readr_2.1.4
[7] tidyr_1.3.0
[8] tibble_3.2.1
[9] tidyverse_2.0.0
[10] scales_1.2.1
[11] RobustRegressions_1.5.1
[12] robCompositions_2.3.1
[13] data.table_1.14.8
[14] pls_2.8-2
[15] rio_0.5.29
[16] Plots_1.3
[17] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
[18] minfi_1.46.0
[19] bumphunter_1.42.0
[20] locfit_1.5-9.8
[21] iterators_1.0.14
[22] foreach_1.5.2
[23] Biostrings_2.68.1
[24] XVector_0.40.0
[25] SummarizedExperiment_1.30.2
[26] Biobase_2.60.0
[27] MatrixGenerics_1.12.2
[28] matrixStats_1.0.0
[29] GenomicRanges_1.52.0
[30] GenomeInfoDb_1.36.1
[31] IRanges_2.34.1
[32] S4Vectors_0.38.1
[33] BiocGenerics_0.46.0
[34] magrittr_2.0.3
[35] janitor_2.2.0
[36] Hmisc_5.1-0
[37] here_1.0.1
[38] Helpers_0.1.0
[39] ggrepel_0.9.3
[40] ggpubr_0.6.0
[41] DMR_0.1.3
[42] ccmm_1.0
[43] bacon_1.28.0
[44] ellipse_0.5.0
[45] BiocParallel_1.34.2
[46] ggplot2_3.4.2
loaded via a namespace (and not attached):
[1] dichromat_2.0-0.1 progress_1.2.2
[3] pacman_0.5.1 nnet_7.3-19
[5] HDF5Array_1.28.1 TH.data_1.1-2
[7] vctrs_0.6.3 digest_0.6.33
[9] png_0.1-8 proxy_0.4-27
[11] pcaPP_2.0-3 corrplot_0.92
[13] deldir_1.0-9 renv_1.0.0
[15] hdrcde_3.4 MASS_7.3-60
[17] reshape_0.8.9 withr_2.5.0
[19] psych_2.3.6 xfun_0.39
[21] survival_3.5-5 doRNG_1.8.6
[23] memoise_2.0.1 diptest_0.76-0
[25] MatrixModels_0.5-2 zoo_1.8-12
[27] DEoptimR_1.1-0 Formula_1.2-5
[29] prettyunits_1.1.1 GGally_2.1.2
[31] prabclus_2.3-2 KEGGREST_1.40.0
[33] httr_1.4.6 bigparallelr_0.3.2
[35] rstatix_0.7.2 restfulr_0.0.15
[37] hash_2.2.6.2 cvTools_0.3.2
[39] rhdf5filters_1.12.1 fpc_2.2-10
[41] rhdf5_2.44.0 rstudioapi_0.15.0
[43] generics_0.1.3 base64enc_0.1-3
[45] curl_5.0.1 sfsmisc_1.1-15
[47] mitools_2.4 zlibbioc_1.46.0
[49] GenomeInfoDbData_1.2.10 quadprog_1.5-8
[51] rms_6.7-0 doParallel_1.0.17
[53] xtable_1.8-4 pracma_2.4.2
[55] evaluate_0.21 S4Arrays_1.0.5
[57] BiocFileCache_2.8.0 preprocessCore_1.62.1
[59] hms_1.1.3 colorspace_2.1-0
[61] filelock_1.0.2 readxl_1.4.3
[63] flexmix_2.3-19 lmtest_0.9-40
[65] snakecase_0.11.0 modeltools_0.2-23
[67] lattice_0.21-8 genefilter_1.82.1
[69] robustbase_0.99-0 SparseM_1.81
[71] cowplot_1.1.1 survey_4.2-1
[73] XML_3.99-0.14 class_7.3-22
[75] pillar_1.9.0 nlme_3.1-162
[77] compiler_4.3.1 stringi_1.7.12
[79] GenomicAlignments_1.36.0 plyr_1.8.8
[81] fda_6.1.4 crayon_1.5.2
[83] abind_1.4-5 BiocIO_1.10.0
[85] truncnorm_1.0-9 flock_0.7
[87] haven_2.5.3 sp_2.0-0
[89] bit_4.0.5 sandwich_3.0-2
[91] multcomp_1.4-25 bigassertr_0.1.6
[93] codetools_0.2-19 perry_0.3.1
[95] openssl_2.1.0 ggfortify_0.4.16
[97] e1071_1.7-13 biovizBase_1.48.0
[99] fds_1.8 multtest_2.56.0
[101] splines_4.3.1 Rcpp_1.0.11
[103] fastDummies_1.7.3 quantreg_5.96
[105] dbplyr_2.3.3 sparseMatrixStats_1.12.2
[107] cellranger_1.1.0 interp_1.1-4
[109] knitr_1.43 blob_1.2.4
[111] utf8_1.2.3 AnnotationFilter_1.24.0
[113] checkmate_2.2.0 DelayedMatrixStats_1.22.1
[115] Gviz_1.44.0 openxlsx_4.2.5.2
[117] ggsignif_0.6.4 Matrix_1.6-0
[119] tzdb_0.4.0 pkgconfig_2.0.3
[121] tools_4.3.1 cachem_1.0.8
[123] RSQLite_2.3.1 NADA_1.6-1.1
[125] DBI_1.1.3 fastmap_1.1.1
[127] rmarkdown_2.23 grid_4.3.1
[129] Rsamtools_2.16.0 broom_1.0.5
[131] xlsx_0.6.5 BiocManager_1.30.21.1
[133] VariantAnnotation_1.46.0 carData_3.0-5
[135] scrime_1.3.5 rpart_4.1.19
[137] yaml_2.3.7 deSolve_1.36
[139] latticeExtra_0.6-30 foreign_0.8-84
[141] rtracklayer_1.60.0 illuminaio_0.42.0
[143] cli_3.6.1 siggenes_1.74.0
[145] GEOquery_2.68.0 lifecycle_1.0.3
[147] askpass_1.1 rainbow_3.7
[149] mvtnorm_1.2-2 kernlab_0.9-32
[151] backports_1.4.1 annotate_1.78.0
[153] timechange_0.2.0 gtable_0.3.3
[155] rjson_0.2.21 ggridges_0.5.4
[157] limma_3.56.2 bitops_1.0-7
[159] bit64_4.0.5 base64_2.0.1
[161] zip_2.3.0 ranger_0.15.1
[163] polspline_1.1.23 rrcov_1.7-4
[165] coMET_1.32.0 lazyeval_0.2.2
[167] bigstatsr_1.5.12 zCompositions_1.4.0-1
[169] htmltools_0.5.5 rJava_1.0-6
[171] rappdirs_0.3.3 ensembldb_2.24.0
[173] glue_1.6.2 VIM_6.2.2
[175] RCurl_1.98-1.12 rprojroot_2.0.3
[177] mclust_6.0.0 ks_1.14.0
[179] mnormt_2.1.1 BSgenome_1.68.0
[181] jpeg_0.1-10 gridExtra_2.3
[183] boot_1.3-28.1 R6_2.5.1
[185] vcd_1.4-11 xlsxjars_0.6.1
[187] GenomicFeatures_1.52.1 cluster_2.1.4
[189] rngtools_1.5.2 Rhdf5lib_1.22.0
[191] beanplot_1.3.1 robustHD_0.7.4
[193] DelayedArray_0.26.6 tidyselect_1.2.0
[195] ProtGenerics_1.32.0 htmlTable_2.4.1
[197] xml2_1.3.5 QCEWAS_1.2-3
[199] car_3.1-2 AnnotationDbi_1.62.2
[201] munsell_0.5.0 KernSmooth_2.23-22
[203] laeken_0.5.2 nor1mix_1.3-0
[205] htmlwidgets_1.6.2 RColorBrewer_1.1-3
[207] biomaRt_2.56.1 rlang_1.1.1
[209] fansi_1.0.4