Processing information in `mass_data` class object
Xiaotao Shen
Created on 2021-12-04 and updated on 2026-03-02
Source:vignettes/process_info.Rmd
process_info.RmdData preparation
In mass_dataset class object, it contains all the
processing information in it. We can trace the analysis and parameters
so we can do the reproducible analysis.
library(massdataset)
data("expression_data")
data("sample_info")
data("variable_info")
object =
create_mass_dataset(
expression_data = expression_data,
sample_info = sample_info,
variable_info = variable_info
)
library(tidyverse)
object =
object %>%
activate_mass_dataset(what = "expression_data") %>%
filter(!is.na(QC_1))
object =
object %>%
activate_mass_dataset(what = "expression_data") %>%
filter(!is.na(QC_2))
object =
object %>%
mutate_mean_intensity()
object =
object %>%
mutate_median_intensity() %>%
mutate_rsd()process_info
process_info = extract_process_info(object)
process_info
#> $create_mass_dataset
#> --------------------
#> pacakge_name: massdataset
#> function_name: create_mass_dataset()
#> time: 2026-03-02 09:28:24.028827
#> parameters:
#> no : no
#>
#> $filter
#> $filter[[1]]
#> --------------------
#> pacakge_name: massdataset
#> function_name: filter()
#> time: 2026-03-02 09:28:24.161025
#> parameters:
#> parameter : `~!is.na(QC_1)`
#>
#> $filter[[2]]
#> --------------------
#> pacakge_name: massdataset
#> function_name: filter()
#> time: 2026-03-02 09:28:24.161968
#> parameters:
#> parameter : `~!is.na(QC_2)`
#>
#>
#> $mutate_mean_intensity
#> --------------------
#> pacakge_name: massdataset
#> function_name: mutate_mean_intensity()
#> time: 2026-03-02 09:28:24.164592
#> parameters:
#> according_to_samples : c("Blank_3", "Blank_4", "QC_1", "QC_2", "PS4P1", "PS4P2", "PS4P3", "PS4P4")
#>
#> $mutate_median_intensity
#> --------------------
#> pacakge_name: massdataset
#> function_name: mutate_median_intensity()
#> time: 2026-03-02 09:28:24.171697
#> parameters:
#> according_to_samples : c("Blank_3", "Blank_4", "QC_1", "QC_2", "PS4P1", "PS4P2", "PS4P3", "PS4P4")
#>
#> $mutate_rsd
#> --------------------
#> pacakge_name: massdataset
#> function_name: mutate_rsd()
#> time: 2026-03-02 09:28:24.175625
#> parameters:
#> according_to_samples : c("Blank_3", "Blank_4", "QC_1", "QC_2", "PS4P1", "PS4P2", "PS4P3", "PS4P4")The process_info contains all the steps which are ordered by time.
process_info$mutate_median_intensity
#> --------------------
#> pacakge_name: massdataset
#> function_name: mutate_median_intensity()
#> time: 2026-03-02 09:28:24.171697
#> parameters:
#> according_to_samples : c("Blank_3", "Blank_4", "QC_1", "QC_2", "PS4P1", "PS4P2", "PS4P3", "PS4P4")
process_info$mutate_median_intensity@parameter
#> $according_to_samples
#> [1] "Blank_3" "Blank_4" "QC_1" "QC_2" "PS4P1" "PS4P2" "PS4P3"
#> [8] "PS4P4"Session information
sessionInfo()
#> R version 4.5.2 (2025-10-31)
#> Platform: aarch64-apple-darwin20
#> Running under: macOS Tahoe 26.3
#>
#> Matrix products: default
#> BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
#>
#> locale:
#> [1] C.UTF-8/C.UTF-8/C.UTF-8/C/C.UTF-8/C.UTF-8
#>
#> time zone: Asia/Singapore
#> tzcode source: internal
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1 purrr_1.1.0
#> [5] readr_2.1.5 tidyr_1.3.1 tibble_3.3.0 tidyverse_2.0.0
#> [9] magrittr_2.0.3 dplyr_1.1.4 ggplot2_4.0.2 massdataset_0.99.1
#>
#> loaded via a namespace (and not attached):
#> [1] tidyselect_1.2.1 farver_2.1.2
#> [3] S7_0.2.0 fastmap_1.2.0
#> [5] digest_0.6.37 timechange_0.3.0
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#> [19] abind_1.4-8 withr_3.0.2
#> [21] BiocGenerics_0.54.0 desc_1.4.3
#> [23] grid_4.5.2 stats4_4.5.2
#> [25] colorspace_2.1-1 scales_1.4.0
#> [27] iterators_1.0.14 dichromat_2.0-0.1
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#> [39] cachem_1.1.0 parallel_4.5.2
#> [41] XVector_0.48.0 matrixStats_1.5.0
#> [43] vctrs_0.6.5 Matrix_1.7-4
#> [45] jsonlite_2.0.0 IRanges_2.42.0
#> [47] hms_1.1.3 GetoptLong_1.0.5
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#> [75] openxlsx_4.2.8 bslib_0.9.0
#> [77] Rcpp_1.1.0 zip_2.3.3
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#> [81] fs_1.6.6 MatrixGenerics_1.20.0
#> [83] pkgconfig_2.0.3 GlobalOptions_0.1.2