{ "_id": "6a106dccacfb0bcc41caafe6", "Package": "rplec", "Title": "Placental Epigenetic Clock to Estimate Aging by DNA Methylation", "Version": "0.1.3", "Authors@R": "c(person(\ngiven = \"Herdiantri\"\n,family = \"Sufriyana\"\n,email = \"herdi@nycu.edu.tw\"\n,role = c(\"aut\", \"cre\")\n,comment = c(ORCID = \"0000-0001-9178-0222\")\n)\n,person(\ngiven = \"Emily Chia-Yu\"\n,family = \"Su\"\n,email = \"emily@nycu.edu.tw\"\n,role = c(\"aut\")\n,comment = c(ORCID = \"0000-0003-4801-5159\")\n)\n)", "Description": "Placental epigenetic clock to estimate aging based on\ngestational age using DNA methylation levels, so called\nplacental epigenetic clock (PlEC). We developed a PlEC for the\n2024 Placental Clock DREAM Challenge\n().\nOur PlEC achieved the top performance based on an independent\ntest set. PlEC can be used to identify accelerated/decelerated\naging of placenta for understanding placental\ndysfunction-related conditions, e.g., great obstetrical\nsyndromes including preeclampsia, fetal growth restriction,\npreterm labor, preterm premature rupture of the membranes, late\nspontaneous abortion, and placental abruption. Detailed\nmethodologies and examples are documented in our vignette,\navailable at\n.", "VignetteBuilder": "knitr", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "LazyData": "true", "LazyDataCompression": "xz", "Config/testthat/edition": "3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-07 08:14:50 UTC", "User": "root" }, "Author": "Herdiantri Sufriyana [aut, cre]\n(), Emily Chia-Yu Su\n[aut] ()", "Maintainer": "Herdiantri Sufriyana ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2025-01-27 18:30:05 UTC", "RemoteUrl": "https://github.com/cran/rplec", "RemoteRef": "HEAD", "RemoteSha": "85b4f36a2243d66740dc3506c64be44750599d19", "MD5sum": "bffb53512517f7109b39a72fb37b06f1", "_user": "cran", "_type": "src", "_file": "rplec_0.1.3.tar.gz", "_fileid": "f70203a443214741c75e71478bcb9de1e5c2186ba2aa8e2968e219c3bd725ad8", "_filesize": 3363544, "_sha256": "f70203a443214741c75e71478bcb9de1e5c2186ba2aa8e2968e219c3bd725ad8", "_created": "2026-05-07T08:14:50.000Z", "_published": "2026-05-22T14:53:00.243Z", "_distro": "noble", "_jobs": [ { "job": 77404317279, "time": 225, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6850189572" }, { "job": 77404317256, "time": 193, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6850187273" }, { "job": 77404316379, "time": 292, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6850127296" }, { "job": 77404316246, "time": 141, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7163484897" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/25483858181", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/rplec", "_commit": { "id": "85b4f36a2243d66740dc3506c64be44750599d19", "author": "Herdiantri Sufriyana ", "committer": "cran-robot ", "message": "version 0.1.3\n", "time": 1738002605 }, "_maintainer": { "name": "Herdiantri Sufriyana", "email": "herdi@nycu.edu.tw", "orcid": "0000-0001-9178-0222" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4", "role": "Depends" }, { "package": "doParallel", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "pbapply", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "RPMM", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "tidyverse", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 165, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rplec" }, "_searchresults": 4, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/rplec.html", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "0.1.3", "date": "2025-01-27" } ], "_exports": [ "bmiq_norm_450k", "download_beta_values_case", "download_beta_values_control", "ipla", "plec", "qc" ], "_datasets": [ { "name": "aging", "title": "Residual DNA-methylation-based (DNAm) gestational age", "object": "aging", "class": [ "data.frame" ], "fields": [ "output" ], "rows": 10, "table": true, "tojson": true }, { "name": "beta_v_indices", "title": "Indices for random beta values", "object": "beta_v_indices", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "ga", "title": "Gestational age for both case and control groups", "object": "ga", "class": [ "data.frame" ], "fields": [ "GA" ], "rows": 10, "table": true, "tojson": true }, { "name": "phenotype", "title": "Phenotype for both case and control groups", "object": "phenotype", "class": [ "data.frame" ], "fields": [ "phenotype" ], "rows": 10, "table": true, "tojson": true }, { "name": "plec_int_coef", "title": "Intercept and coefficients of placental epigenetic clock", "object": "plec_int_coef", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "predictor", "ga_est", "fgr_pred", "pe_pred", "pe_onset_pred", "preterm_pred", "anencephaly_pred", "spina_bifida_pred", "gdm_pred", "diandric_triploid_pred", "miscarriage_pred", "lga_pred", "subfertility_pred", "hellp_pred", "chorioamnionitis_pred", "ga_res_conds_fgr_est", "ga_res_conds_pe_est", "ga_res_conds_pe_onset_est", "ga_res_conds_preterm_est", "ga_res_conds_anencephaly_est", "ga_res_conds_spina_bifida_est", "ga_res_conds_gdm_est", "ga_res_conds_diandric_triploid_est", "ga_res_conds_miscarriage_est", "ga_res_conds_lga_est", "ga_res_conds_subfertility_est", "ga_res_conds_hellp_est", "ga_res_conds_chorioamnionitis_est", "ga_res_conds_pred_est", "ga_res_comb_pr_est", "ga_res_comb_tb_est", "ga_res_comb_ta_est" ], "rows": 10447, "table": true, "tojson": true }, { "name": "plec_scaler_mean", "title": "Mean values of the scalers of placental epigenetic clock", "object": "plec_scaler_mean", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "predictor", "ga_est", "fgr_pred", "pe_pred", "pe_onset_pred", "preterm_pred", "anencephaly_pred", "spina_bifida_pred", "gdm_pred", "diandric_triploid_pred", "miscarriage_pred", "lga_pred", "subfertility_pred", "hellp_pred", "chorioamnionitis_pred", "ga_res_conds_fgr_est", "ga_res_conds_pe_est", "ga_res_conds_pe_onset_est", "ga_res_conds_preterm_est", "ga_res_conds_anencephaly_est", "ga_res_conds_spina_bifida_est", "ga_res_conds_gdm_est", "ga_res_conds_diandric_triploid_est", "ga_res_conds_miscarriage_est", "ga_res_conds_lga_est", "ga_res_conds_subfertility_est", "ga_res_conds_hellp_est", "ga_res_conds_chorioamnionitis_est", "ga_res_conds_pred_est", "ga_res_comb_pr_est", "ga_res_comb_tb_est", "ga_res_comb_ta_est" ], "rows": 10446, "table": true, "tojson": true }, { "name": "plec_scaler_scale", "title": "Scale values of the scalers of placental epigenetic clock", "object": "plec_scaler_scale", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "predictor", "ga_est", "fgr_pred", "pe_pred", "pe_onset_pred", "preterm_pred", "anencephaly_pred", "spina_bifida_pred", "gdm_pred", "diandric_triploid_pred", "miscarriage_pred", "lga_pred", "subfertility_pred", "hellp_pred", "chorioamnionitis_pred", "ga_res_conds_fgr_est", "ga_res_conds_pe_est", "ga_res_conds_pe_onset_est", "ga_res_conds_preterm_est", "ga_res_conds_anencephaly_est", "ga_res_conds_spina_bifida_est", "ga_res_conds_gdm_est", "ga_res_conds_diandric_triploid_est", "ga_res_conds_miscarriage_est", "ga_res_conds_lga_est", "ga_res_conds_subfertility_est", "ga_res_conds_hellp_est", "ga_res_conds_chorioamnionitis_est", "ga_res_conds_pred_est", "ga_res_comb_pr_est", "ga_res_comb_tb_est", "ga_res_comb_ta_est" ], "rows": 10446, "table": true, "tojson": true }, { "name": "probe_info_450k", "title": "Probe info for 450K", "object": "probe_info_450k", "class": [ "list" ], "fields": [], "table": true, "tojson": true } ], "_help": [ { "page": "aging", "title": "Residual DNA-methylation-based (DNAm) gestational age", "topics": [ "aging" ] }, { "page": "beta_v_indices", "title": "Indices for random beta values", "topics": [ "beta_v_indices" ] }, { "page": "bmiq_norm_450k", "title": "Normalize DNA methylation values", "topics": [ "bmiq_norm_450k" ] }, { "page": "download_beta_values_case", "title": "Access Beta values at individual CpG sites for case group", "topics": [ "download_beta_values_case" ] }, { "page": "download_beta_values_control", "title": "Access Beta values at individual CpG sites for control group", "topics": [ "download_beta_values_control" ] }, { "page": "ga", "title": "Gestational age for both case and control groups", "topics": [ "ga" ] }, { "page": "ipla", "title": "Identify placental aging", "topics": [ "ipla" ] }, { "page": "phenotype", "title": "Phenotype for both case and control groups", "topics": [ "phenotype" ] }, { "page": "plec", "title": "Estimate DNA-methylation-based gestational age", "topics": [ "plec" ] }, { "page": "plec_int_coef", "title": "Intercept and coefficients of placental epigenetic clock", "topics": [ "plec_int_coef" ] }, { "page": "plec_scaler_mean", "title": "Mean values of the scalers of placental epigenetic clock", "topics": [ "plec_scaler_mean" ] }, { "page": "plec_scaler_scale", "title": "Scale values of the scalers of placental epigenetic clock", "topics": [ "plec_scaler_scale" ] }, { "page": "probe_info_450k", "title": "Probe info for 450K", "topics": [ "probe_info_450k" ] }, { "page": "qc", "title": "Perform quality control", "topics": [ "qc" ] } ], "_readme": "https://github.com/cran/rplec/raw/HEAD/README.md", "_rundeps": [ "cli", "cluster", "codetools", "cpp11", "doParallel", "dplyr", "farver", "foreach", "generics", "ggplot2", "glue", "gtable", "isoband", "iterators", "labeling", "lifecycle", "magrittr", "pbapply", "pillar", "pkgconfig", "purrr", "R6", "RColorBrewer", "rlang", "RPMM", "S7", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "placental_aging_analysis.Rmd", "filename": "placental_aging_analysis.html", "title": "Placental Aging Analysis", "author": "Herdiantri Sufriyana, Emily Chia-Yu Su", "engine": "knitr::rmarkdown", "headings": [ "Programming environment", "Data preprocessing", "Quality control", "Identifying placental aging" ], "created": "2025-01-27 18:30:05", "modified": "2025-01-27 18:30:05", "commits": 1 } ], "_score": 2.6989700043360187, "_indexed": true, "_nocasepkg": "rplec", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.3", "date": "2026-05-07T08:17:36.000Z", "distro": "noble", "commit": "85b4f36a2243d66740dc3506c64be44750599d19", "fileid": "6ab00fb911a3cdd71bd4fad15269f5d2ef633140a725727ce17932a2172d4e95", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25483858181" }, { "r": "4.6.0", "os": "linux", "version": "0.1.3", "date": "2026-05-07T08:17:23.000Z", "distro": "noble", "commit": "85b4f36a2243d66740dc3506c64be44750599d19", "fileid": "b8634ba23aaffdd8cb23c22afe37d4ee6dafc8c70260877f4ea0b0f5a757d280", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25483858181" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.3", "date": "2026-05-22T14:52:32.000Z", "commit": "85b4f36a2243d66740dc3506c64be44750599d19", "fileid": "e50537adde739b637848e2244c0da807879b33c3e6feaa5352a78b07de6bff7f", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/25483858181" } ] }