Placental Aging Analysis

Institute of Biomedical Informatics, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
herdi@nycu.edu.tw

Institute of Biomedical Informatics, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.

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)

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

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

sessionInfo()

## R version 4.4.1 (2024-06-14)
## Platform: aarch64-unknown-linux-gnu
## Running under: Ubuntu 22.04.5 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [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_1.8.9    highr_0.11        dplyr_1.1.4      
##  [5] compiler_4.4.1    tidyselect_1.2.1  RPMM_1.25         stringr_1.5.1    
##  [9] parallel_4.4.1    tidyr_1.3.1       cluster_2.1.6     jquerylib_0.1.4  
## [13] scales_1.3.0      yaml_2.3.10       fastmap_1.2.0     ggplot2_3.5.1    
## [17] R6_2.5.1          labeling_0.4.3    generics_0.1.3    knitr_1.48       
## [21] iterators_1.0.14  tibble_3.2.1      munsell_0.5.1     bslib_0.8.0      
## [25] pillar_1.9.0      rlang_1.1.4       utf8_1.2.4        stringi_1.8.4    
## [29] cachem_1.1.0      xfun_0.48         sass_0.4.9        doParallel_1.0.17
## [33] cli_3.6.3         withr_3.0.2       magrittr_2.0.3    digest_0.6.37    
## [37] foreach_1.5.2     grid_4.4.1        pbapply_1.7-2     rstudioapi_0.17.1
## [41] lifecycle_1.0.4   vctrs_0.6.5       evaluate_1.0.1    glue_1.8.0       
## [45] farver_2.1.2      codetools_0.2-20  fansi_1.0.6       colorspace_2.1-1 
## [49] purrr_1.0.2       rmarkdown_2.28    tools_4.4.1       pkgconfig_2.0.3  
## [53] htmltools_0.5.8.1