Programming environment | Data preprocessing | Quality control | Identifying placental aging
Package: rplec 0.1.3
Herdiantri Sufriyana
rplec: Placental Epigenetic Clock to Estimate Aging by DNA Methylation
Placental epigenetic clock to estimate aging based on gestational age using DNA methylation levels, so called placental epigenetic clock (PlEC). We developed a PlEC for the 2024 Placental Clock DREAM Challenge (<https://www.synapse.org/Synapse:syn59520082/wiki/628063>). Our PlEC achieved the top performance based on an independent test set. PlEC can be used to identify accelerated/decelerated aging of placenta for understanding placental dysfunction-related conditions, e.g., great obstetrical syndromes including preeclampsia, fetal growth restriction, preterm labor, preterm premature rupture of the membranes, late spontaneous abortion, and placental abruption. Detailed methodologies and examples are documented in our vignette, available at <https://herdiantrisufriyana.github.io/rplec/doc/placental_aging_analysis.html>.
Authors:
rplec_0.1.3.tar.gz
rplec_0.1.3.tar.gz(r-4.7-any)rplec_0.1.3.tar.gz(r-4.6-any)
rplec_0.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
rplec/json (API)
| # Install 'rplec' in R: |
| install.packages('rplec', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- aging - Residual DNA-methylation-based (DNAm) gestational age
- beta_v_indices - Indices for random beta values
- ga - Gestational age for both case and control groups
- phenotype - Phenotype for both case and control groups
- plec_int_coef - Intercept and coefficients of placental epigenetic clock
- plec_scaler_mean - Mean values of the scalers of placental epigenetic clock
- plec_scaler_scale - Scale values of the scalers of placental epigenetic clock
- probe_info_450k - Probe info for 450K
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:85b4f36a22. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 206 | ||
| source / vignettes | OK | 273 | ||
| linux-release-x86_64 | OK | 210 | ||
| wasm-release | OK | 141 |
Exports:bmiq_norm_450kdownload_beta_values_casedownload_beta_values_controliplaplecqc
Dependencies:cliclustercodetoolscpp11doParalleldplyrfarverforeachgenericsggplot2gluegtableisobanditeratorslabelinglifecyclemagrittrpbapplypillarpkgconfigpurrrR6RColorBrewerrlangRPMMS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Residual DNA-methylation-based (DNAm) gestational age | aging |
| Indices for random beta values | beta_v_indices |
| Normalize DNA methylation values | bmiq_norm_450k |
| Access Beta values at individual CpG sites for case group | download_beta_values_case |
| Access Beta values at individual CpG sites for control group | download_beta_values_control |
| Gestational age for both case and control groups | ga |
| Identify placental aging | ipla |
| Phenotype for both case and control groups | phenotype |
| Estimate DNA-methylation-based gestational age | plec |
| Intercept and coefficients of placental epigenetic clock | plec_int_coef |
| Mean values of the scalers of placental epigenetic clock | plec_scaler_mean |
| Scale values of the scalers of placental epigenetic clock | plec_scaler_scale |
| Probe info for 450K | probe_info_450k |
| Perform quality control | qc |