Skip to content

fredlandfors/VIPVIZA-LPL

master
Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
out
 
 
src
 
 
 
 
 
 
 
 
 
 

VIPVIZA-LPL

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

About

No description, website, or topics provided.

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages