Date: 2025-01-10

# Placental Aging Analysis

#### Herdiantri Sufriyana

#### Emily Chia-Yu Su

# 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