Programming environment

library(rplec)

Data preprocessing

beta_values_case <- download_beta_values_case()
beta_values_control <- download_beta_values_control()
data(ga)
data(phenotype)

norm_beta_values_case <- bmiq_norm_450k(beta_values_case)
norm_beta_values_control <- bmiq_norm_450k(beta_values_control)

Quality control

dnam_ga_case <- plec(norm_beta_values_case)
dnam_ga_control <- plec(norm_beta_values_control)
dnam_ga <- rbind(dnam_ga_case, dnam_ga_control)

set.seed(1)
plec_qc <- qc(dnam_ga, ga, phenotype)

Identifying placental aging

aging_case <- plec(norm_beta_values_case, type = "residual")
aging_control <- plec(norm_beta_values_control, type = "residual")
aging <- rbind(aging_case, aging_control)

set.seed(1)
ipla_results <- ipla(aging, ga, phenotype)

## Warning: Removed 4 rows containing missing values or values outside the scale range
## (`geom_ribbon()`).

set.seed(1)
ipla_stats <- ipla(aging, ga, phenotype, method = "Mann-Whitney U")

## Warning: Removed 4 rows containing missing values or values outside the scale range
## (`geom_ribbon()`).

set.seed(1)
ipla_stats_5_20 <-
  ipla(aging, ga, phenotype, method = "Mann-Whitney U", from = 5, to = 20)

## Warning: Removed 4 rows containing missing values or values outside the scale range
## (`geom_ribbon()`).

sessionInfo()

## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] rplec_0.1.3
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.6       jsonlite_2.0.0     dplyr_1.2.1        compiler_4.6.1    
##  [5] tidyselect_1.2.1   RPMM_1.25          stringr_1.6.0      parallel_4.6.1    
##  [9] tidyr_1.3.2        cluster_2.1.8.2    jquerylib_0.1.4    scales_1.4.0      
## [13] yaml_2.3.12        fastmap_1.2.0      ggplot2_4.0.3      R6_2.6.1          
## [17] labeling_0.4.3     generics_0.1.4     knitr_1.51         iterators_1.0.14  
## [21] tibble_3.3.1       maketools_1.3.2    RColorBrewer_1.1-3 bslib_0.11.0      
## [25] pillar_1.11.1      rlang_1.3.0        stringi_1.8.7      cachem_1.1.0      
## [29] xfun_0.59          S7_0.2.2           sass_0.4.10        sys_3.4.3         
## [33] otel_0.2.0         doParallel_1.0.17  cli_3.6.6          withr_3.0.3       
## [37] magrittr_2.0.5     digest_0.6.39      foreach_1.5.2      grid_4.6.1        
## [41] pbapply_1.7-4      lifecycle_1.0.5    vctrs_0.7.3        evaluate_1.0.5    
## [45] glue_1.8.1         farver_2.1.2       codetools_0.2-20   buildtools_1.0.0  
## [49] purrr_1.2.2        rmarkdown_2.31     tools_4.6.1        pkgconfig_2.0.3   
## [53] htmltools_0.5.9