Scaling

Xiaotao Shen (https://www.shenxt.info/)

Created on 2022-02-18 and updated on 2022-09-19

Source: vignettes/scale_data.Rmd

Data preparation 

library(massdataset)
library(tidyverse)
library(massstat)
data("liver_aging_pos")
liver_aging_pos
#> -------------------- 
#> massdataset version: 0.01 
#> -------------------- 
#> 1.expression_data:[ 21607 x 24 data.frame]
#> 2.sample_info:[ 24 x 4 data.frame]
#> 3.variable_info:[ 21607 x 3 data.frame]
#> 4.sample_info_note:[ 4 x 2 data.frame]
#> 5.variable_info_note:[ 3 x 2 data.frame]
#> 6.ms2_data:[ 0 variables x 0 MS2 spectra]
#> -------------------- 
#> Processing information (extract_process_info())
#> Creation ---------- 
#>       Package         Function.used                Time
#> 1 massdataset create_mass_dataset() 2021-12-23 00:24:02

Scaling 

liver_aging_pos[1,] %>% 
  scale_data(center = TRUE, method = "auto") %>% 
  extract_expression_data() %>% 
  as.numeric() %>% 
  density() %>% 
  plot()

liver_aging_pos[1,] %>% 
  scale_data(center = TRUE, method = "range") %>% 
  extract_expression_data() %>% 
  as.numeric() %>% 
  density() %>% 
  plot()

liver_aging_pos[1,] %>% 
  scale_data(center = TRUE, method = "pareto") %>% 
  extract_expression_data() %>% 
  as.numeric() %>% 
  density() %>% 
  plot()

Session information 

sessionInfo()
#> R version 4.1.2 (2021-11-01)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur 10.16
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#>  [1] ggfortify_0.4.14   massstat_0.99.4    forcats_0.5.1      stringr_1.4.0     
#>  [5] dplyr_1.0.7        purrr_0.3.4        readr_2.1.1        tidyr_1.1.4       
#>  [9] tibble_3.1.6       ggplot2_3.3.5      tidyverse_1.3.1    magrittr_2.0.2    
#> [13] masstools_0.99.3   massdataset_0.99.6
#> 
#> loaded via a namespace (and not attached):
#>   [1] readxl_1.3.1          snow_0.4-4            backports_1.4.1      
#>   [4] circlize_0.4.14       systemfonts_1.0.3     igraph_1.2.11        
#>   [7] plyr_1.8.6            lazyeval_0.2.2        BiocParallel_1.28.3  
#>  [10] crosstalk_1.2.0       leaflet_2.0.4.1       digest_0.6.29        
#>  [13] foreach_1.5.1         yulab.utils_0.0.4     htmltools_0.5.2      
#>  [16] fansi_1.0.2           memoise_2.0.1         cluster_2.1.2        
#>  [19] doParallel_1.0.16     tzdb_0.2.0            openxlsx_4.2.5       
#>  [22] limma_3.50.0          ComplexHeatmap_2.10.0 modelr_0.1.8         
#>  [25] matrixStats_0.61.0    rARPACK_0.11-0        pkgdown_2.0.2        
#>  [28] colorspace_2.0-2      rvest_1.0.2           ggrepel_0.9.1        
#>  [31] textshaping_0.3.6     haven_2.4.3           xfun_0.29            
#>  [34] crayon_1.4.2          jsonlite_1.7.3        impute_1.68.0        
#>  [37] iterators_1.0.13      glue_1.6.1            gtable_0.3.0         
#>  [40] zlibbioc_1.40.0       GetoptLong_1.0.5      shape_1.4.6          
#>  [43] BiocGenerics_0.40.0   scales_1.1.1          vsn_3.62.0           
#>  [46] DBI_1.1.2             Rcpp_1.0.8            mzR_2.28.0           
#>  [49] viridisLite_0.4.0     clue_0.3-60           gridGraphics_0.5-1   
#>  [52] preprocessCore_1.56.0 clisymbols_1.2.0      stats4_4.1.2         
#>  [55] MsCoreUtils_1.6.0     htmlwidgets_1.5.4     httr_1.4.2           
#>  [58] RColorBrewer_1.1-2    ellipsis_0.3.2        pkgconfig_2.0.3      
#>  [61] XML_3.99-0.8          sass_0.4.0            dbplyr_2.1.1         
#>  [64] utf8_1.2.2            reshape2_1.4.4        ggplotify_0.1.0      
#>  [67] tidyselect_1.1.1      rlang_1.0.0           munsell_0.5.0        
#>  [70] cellranger_1.1.0      tools_4.1.2           cachem_1.0.6         
#>  [73] cli_3.1.1             generics_0.1.1        broom_0.7.12         
#>  [76] evaluate_0.14         fastmap_1.1.0         mzID_1.32.0          
#>  [79] yaml_2.2.2            ragg_1.2.1            knitr_1.37           
#>  [82] fs_1.5.2              zip_2.2.0             ncdf4_1.19           
#>  [85] pbapply_1.5-0         xml2_1.3.3            compiler_4.1.2       
#>  [88] rstudioapi_0.13       plotly_4.10.0         png_0.1-7            
#>  [91] affyio_1.64.0         reprex_2.0.1          bslib_0.3.1          
#>  [94] stringi_1.7.6         highr_0.9             RSpectra_0.16-0      
#>  [97] desc_1.4.0            MSnbase_2.20.4        lattice_0.20-45      
#> [100] Matrix_1.4-0          ProtGenerics_1.26.0   ggsci_2.9            
#> [103] vctrs_0.3.8           pillar_1.6.5          lifecycle_1.0.1      
#> [106] BiocManager_1.30.16   jquerylib_0.1.4       MALDIquant_1.21      
#> [109] GlobalOptions_0.1.2   data.table_1.14.2     corpcor_1.6.10       
#> [112] patchwork_1.1.1       R6_2.5.1              pcaMethods_1.86.0    
#> [115] affy_1.72.0           gridExtra_2.3         IRanges_2.28.0       
#> [118] codetools_0.2-18      fastDummies_1.6.3     MASS_7.3-55          
#> [121] assertthat_0.2.1      rprojroot_2.0.2       rjson_0.2.21         
#> [124] withr_2.4.3           S4Vectors_0.32.3      parallel_4.1.2       
#> [127] hms_1.1.1             mixOmics_6.18.1       grid_4.1.2           
#> [130] rmarkdown_2.11        Biobase_2.54.0        lubridate_1.8.0      
#> [133] ellipse_0.4.2