VIPVIZA-LPL

• Preprocessing
  • NMR
    • A. Pre-imputation diagnostics
    • B. Post-imputation diagnostics
    • C. Outlier analysis
• Session info

Preprocessing

NMR

A. Pre-imputation diagnostics

Percent missing:

## [1] 117  22

##          ID    M_VLDL_P    M_VLDL_L   M_VLDL_PL    M_VLDL_C   M_VLDL_CE 
##   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000 
##   M_VLDL_FC   M_VLDL_TG    S_VLDL_P    S_VLDL_L   S_VLDL_PL    S_VLDL_C 
##   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000 
##   S_VLDL_CE   S_VLDL_FC   S_VLDL_TG   XS_VLDL_P   XS_VLDL_L  XS_VLDL_PL 
##   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000 
##   XS_VLDL_C  XS_VLDL_CE  XS_VLDL_FC  XS_VLDL_TG       IDL_P       IDL_L 
##   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000 
##      IDL_PL       IDL_C      IDL_CE      IDL_FC      IDL_TG     L_LDL_P 
##   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000 
##     L_LDL_L    L_LDL_PL     L_LDL_C    L_LDL_CE    L_LDL_FC    L_LDL_TG 
##   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000 
##     M_LDL_P     M_LDL_L    M_LDL_PL     M_LDL_C    M_LDL_FC    M_LDL_TG 
##   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000 
##    XL_HDL_P    XL_HDL_L   XL_HDL_PL    XL_HDL_C   XL_HDL_CE   XL_HDL_FC 
##   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000 
##   XL_HDL_TG     M_HDL_P     M_HDL_L    M_HDL_PL     M_HDL_C    M_HDL_CE 
##   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000 
##    M_HDL_FC    M_HDL_TG     S_HDL_P     S_HDL_L    S_HDL_PL     S_HDL_C 
##   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000 
##    S_HDL_CE    S_HDL_FC    S_HDL_TG      VLDL_D       LDL_D       HDL_D 
##   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000 
##     Serum_C      VLDL_C   Remnant_C       LDL_C       HDL_C      HDL2_C 
##   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000 
##      HDL3_C        EstC       FreeC    Serum_TG     VLDL_TG      LDL_TG 
##   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000 
##      HDL_TG       TotPG       TG_PG          PC          SM      TotCho 
##   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000 
##       ApoA1        ApoB  ApoB_ApoA1       TotFA       UnSat         DHA 
##   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000 
##          LA        FAw3        FAw6        PUFA        MUFA         SFA 
##   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000 
##      DHA_FA       LA_FA     FAw3_FA     FAw6_FA     PUFA_FA     MUFA_FA 
##   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000   0.0000000 
##      SFA_FA    L_VLDL_P    L_VLDL_L   L_VLDL_PL    L_VLDL_C   L_VLDL_CE 
##   0.0000000   0.9090909   0.9090909   0.9090909   0.9090909   0.9090909 
##   L_VLDL_FC   L_VLDL_TG    M_LDL_CE     S_LDL_P     S_LDL_L    S_LDL_PL 
##   0.9090909   0.9090909   0.9090909   0.9090909   0.9090909   0.9090909 
##     S_LDL_C    S_LDL_CE    S_LDL_FC    S_LDL_TG  XXL_VLDL_P  XXL_VLDL_L 
##   0.9090909   0.9090909   0.9090909   0.9090909   1.8181818   1.8181818 
## XXL_VLDL_PL  XXL_VLDL_C XXL_VLDL_CE XXL_VLDL_FC XXL_VLDL_TG   XL_VLDL_P 
##   1.8181818   1.8181818   1.8181818   1.8181818   1.8181818   1.8181818 
##   XL_VLDL_L  XL_VLDL_PL   XL_VLDL_C  XL_VLDL_CE  XL_VLDL_TG     L_HDL_P 
##   1.8181818   1.8181818   1.8181818   1.8181818   1.8181818   1.8181818 
##     L_HDL_L    L_HDL_PL     L_HDL_C    L_HDL_CE    L_HDL_FC    L_HDL_TG 
##   1.8181818   1.8181818   1.8181818   1.8181818   1.8181818   1.8181818 
##  XL_VLDL_FC 
##   2.7272727

B. Post-imputation diagnostics

C. Outlier analysis

PCA:

Column-wise boxplot:

Session info

## R version 4.0.2 (2020-06-22)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS  10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] sv_SE.UTF-8/sv_SE.UTF-8/sv_SE.UTF-8/C/sv_SE.UTF-8/sv_SE.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] ggplot2_3.3.2
## 
## loaded via a namespace (and not attached):
##  [1] ComplexHeatmap_2.5.5 RColorBrewer_1.1-2   pillar_1.4.6        
##  [4] compiler_4.0.2       tools_4.0.2          digest_0.6.27       
##  [7] clue_0.3-57          evaluate_0.14        lifecycle_0.2.0     
## [10] tibble_3.0.3         gtable_0.3.0         pkgconfig_2.0.3     
## [13] png_0.1-7            rlang_0.4.10         parallel_4.0.2      
## [16] yaml_2.2.1           xfun_0.16            withr_2.3.0         
## [19] cluster_2.1.0        dplyr_1.0.2          stringr_1.4.0       
## [22] knitr_1.29           S4Vectors_0.26.1     generics_0.0.2      
## [25] vctrs_0.3.4          GlobalOptions_0.1.2  IRanges_2.22.2      
## [28] cowplot_1.0.0        stats4_4.0.2         grid_4.0.2          
## [31] tidyselect_1.1.0     glue_1.4.2           R6_2.5.0            
## [34] GetoptLong_1.0.2     rmarkdown_2.6        farver_2.0.3        
## [37] purrr_0.3.4          magrittr_2.0.1       MASS_7.3-52         
## [40] scales_1.1.1         ellipsis_0.3.1       htmltools_0.5.0     
## [43] BiocGenerics_0.34.0  visdat_0.5.3         shape_1.4.4         
## [46] circlize_0.4.10      colorspace_1.4-1     labeling_0.3        
## [49] stringi_1.4.6        munsell_0.5.0        crayon_1.3.4        
## [52] rjson_0.2.20