From 7bbee59f1212878566ec441621ea1563ca381a11 Mon Sep 17 00:00:00 2001
From: grlloyd
The MTBLS79_DatasetExperiment
object included in the
structToolbox
package is a processed version of the MTBLS79
-dataset available in peak matrix processing (pmp) package.
+dataset available in peak matrix processing (pmp) package.
This vignette describes step by step how the structToolbox
version was created from the pmp
version (i.e. ‘Dataset
7:SFPM’ from the Scientific Data publication - https://doi.org/10.1038/sdata.2014.12).
The “Sacurine” dataset needs to be converted to a
-DatasetExperiment
object. The ropls
+DatasetExperiment
object. The ropls
package provides the data as a list containing a
dataMatrix
, sampleMetadata
and
variableMetadata
.
The third plot coloured by gender (C) is identical to Figure 2 of the
-ropls
+ropls
package vignette. The structToolbox
package provides a
range of PCA-related diagnostic plots, including D-statistic, scree, and
loadings plots. These plots can be used to further explore the variance
@@ -1006,7 +1006,7 @@
The plot is similar to fig.3 of the ropls +
The plot is similar to fig.3 of the ropls
vignette. Differences are due to inverted LV axes, a common occurrence
with the NIPALS algorithm (used by both structToolbox
and
ropls
) which depends on how the algorithm is
@@ -2413,7 +2413,7 @@
sessionInfo()
-## R version 4.3.1 (2023-06-16)
+## R version 4.3.2 (2023-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
##
@@ -2434,69 +2434,70 @@ Session Info## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
-## [1] openxlsx_4.2.5.2 cowplot_1.1.1 gridExtra_2.3
-## [4] ggplot2_3.4.4 BiocFileCache_2.8.0 dbplyr_2.3.4
-## [7] ropls_1.32.0 pmp_1.12.0 structToolbox_1.13.5
-## [10] struct_1.12.0 BiocStyle_2.28.1
+## [1] openxlsx_4.2.5.2 cowplot_1.1.3 gridExtra_2.3
+## [4] ggplot2_3.4.4 BiocFileCache_2.10.1 dbplyr_2.4.0
+## [7] ropls_1.34.0 pmp_1.14.0 structToolbox_1.15.1
+## [10] struct_1.14.0 BiocStyle_2.30.0
##
## loaded via a namespace (and not attached):
-## [1] DBI_1.1.3 bitops_1.0-7
-## [3] MultiDataSet_1.28.0 rlang_1.1.1
-## [5] magrittr_2.0.3 e1071_1.7-13
-## [7] matrixStats_1.0.0 compiler_4.3.1
-## [9] RSQLite_2.3.1 systemfonts_1.0.5
-## [11] vctrs_0.6.4 reshape2_1.4.4
-## [13] stringr_1.5.0 pkgconfig_2.0.3
+## [1] DBI_1.2.1 bitops_1.0-7
+## [3] MultiDataSet_1.30.0 rlang_1.1.3
+## [5] magrittr_2.0.3 e1071_1.7-14
+## [7] matrixStats_1.2.0 compiler_4.3.2
+## [9] RSQLite_2.3.5 systemfonts_1.0.5
+## [11] vctrs_0.6.5 reshape2_1.4.4
+## [13] stringr_1.5.1 pkgconfig_2.0.3
## [15] crayon_1.5.2 fastmap_1.1.1
-## [17] XVector_0.40.0 labeling_0.4.3
-## [19] utf8_1.2.3 rmarkdown_2.25
-## [21] itertools_0.1-3 ragg_1.2.6
+## [17] XVector_0.42.0 labeling_0.4.3
+## [19] utf8_1.2.4 rmarkdown_2.25
+## [21] itertools_0.1-3 ragg_1.2.7
## [23] bit_4.0.5 purrr_1.0.2
-## [25] xfun_0.40 MultiAssayExperiment_1.26.0
-## [27] randomForest_4.7-1.1 zlibbioc_1.46.0
-## [29] cachem_1.0.8 GenomeInfoDb_1.36.4
-## [31] jsonlite_1.8.7 progress_1.2.2
-## [33] blob_1.2.4 DelayedArray_0.26.7
-## [35] prettyunits_1.2.0 parallel_4.3.1
-## [37] rols_2.28.0 R6_2.5.1
-## [39] bslib_0.5.1 stringi_1.7.12
-## [41] limma_3.56.2 GenomicRanges_1.52.1
-## [43] jquerylib_0.1.4 Rcpp_1.0.11
-## [45] bookdown_0.35 SummarizedExperiment_1.30.2
-## [47] iterators_1.0.14 knitr_1.44
-## [49] IRanges_2.34.1 Matrix_1.6-1.1
-## [51] tidyselect_1.2.0 abind_1.4-5
-## [53] yaml_2.3.7 codetools_0.2-19
-## [55] curl_5.1.0 doRNG_1.8.6
-## [57] lattice_0.21-8 tibble_3.2.1
-## [59] plyr_1.8.9 withr_2.5.1
-## [61] Biobase_2.60.0 evaluate_0.22
-## [63] ontologyIndex_2.11 desc_1.4.2
-## [65] isoband_0.2.7 proxy_0.4-27
-## [67] zip_2.3.0 filelock_1.0.2
-## [69] pillar_1.9.0 BiocManager_1.30.22
-## [71] MatrixGenerics_1.12.3 rngtools_1.5.2
-## [73] foreach_1.5.2 stats4_4.3.1
-## [75] generics_0.1.3 rprojroot_2.0.3
-## [77] sp_2.1-0 RCurl_1.98-1.12
-## [79] hms_1.1.3 S4Vectors_0.38.2
-## [81] munsell_0.5.0 scales_1.2.1
+## [25] xfun_0.41 MultiAssayExperiment_1.28.0
+## [27] randomForest_4.7-1.1 zlibbioc_1.48.0
+## [29] cachem_1.0.8 GenomeInfoDb_1.38.5
+## [31] jsonlite_1.8.8 progress_1.2.3
+## [33] blob_1.2.4 highr_0.10
+## [35] DelayedArray_0.28.0 prettyunits_1.2.0
+## [37] parallel_4.3.2 rols_2.30.0
+## [39] R6_2.5.1 bslib_0.6.1
+## [41] stringi_1.8.3 limma_3.58.1
+## [43] GenomicRanges_1.54.1 jquerylib_0.1.4
+## [45] Rcpp_1.0.12 bookdown_0.37
+## [47] SummarizedExperiment_1.32.0 iterators_1.0.14
+## [49] knitr_1.45 IRanges_2.36.0
+## [51] Matrix_1.6-1.1 tidyselect_1.2.0
+## [53] abind_1.4-5 yaml_2.3.8
+## [55] codetools_0.2-19 curl_5.2.0
+## [57] doRNG_1.8.6 lattice_0.21-9
+## [59] tibble_3.2.1 plyr_1.8.9
+## [61] withr_3.0.0 Biobase_2.62.0
+## [63] evaluate_0.23 ontologyIndex_2.11
+## [65] desc_1.4.3 isoband_0.2.7
+## [67] proxy_0.4-27 zip_2.3.1
+## [69] filelock_1.0.3 pillar_1.9.0
+## [71] BiocManager_1.30.22 MatrixGenerics_1.14.0
+## [73] rngtools_1.5.2 foreach_1.5.2
+## [75] stats4_4.3.2 generics_0.1.3
+## [77] sp_2.1-2 RCurl_1.98-1.14
+## [79] hms_1.1.3 S4Vectors_0.40.2
+## [81] munsell_0.5.0 scales_1.3.0
## [83] calibrate_1.7.7 class_7.3-22
-## [85] glue_1.6.2 tools_4.3.1
-## [87] fs_1.6.3 grid_4.3.1
-## [89] impute_1.74.1 missForest_1.5
-## [91] colorspace_2.1-0 GenomeInfoDbData_1.2.10
-## [93] cli_3.6.1 textshaping_0.3.7
-## [95] fansi_1.0.5 viridisLite_0.4.2
-## [97] ggthemes_4.2.4 S4Arrays_1.0.6
-## [99] dplyr_1.1.3 pls_2.8-2
-## [101] pcaMethods_1.92.0 gtable_0.3.4
-## [103] sass_0.4.7 digest_0.6.33
-## [105] BiocGenerics_0.46.0 farver_2.1.1
-## [107] memoise_2.0.1 htmltools_0.5.6.1
-## [109] pkgdown_2.0.7 lifecycle_1.0.3
-## [111] httr_1.4.7 qqman_0.1.9
-## [113] bit64_4.0.5 MASS_7.3-60
+## [85] glue_1.7.0 tools_4.3.2
+## [87] fs_1.6.3 grid_4.3.2
+## [89] impute_1.76.0 missForest_1.5
+## [91] colorspace_2.1-0 GenomeInfoDbData_1.2.11
+## [93] cli_3.6.2 textshaping_0.3.7
+## [95] fansi_1.0.6 viridisLite_0.4.2
+## [97] ggthemes_5.0.0 S4Arrays_1.2.0
+## [99] dplyr_1.1.4 pls_2.8-3
+## [101] pcaMethods_1.94.0 gtable_0.3.4
+## [103] sass_0.4.8 digest_0.6.34
+## [105] BiocGenerics_0.48.1 SparseArray_1.2.3
+## [107] farver_2.1.1 memoise_2.0.1
+## [109] htmltools_0.5.7 pkgdown_2.0.7
+## [111] lifecycle_1.0.4 httr_1.4.7
+## [113] statmod_1.5.0 bit64_4.0.5
+## [115] qqman_0.1.9 MASS_7.3-60
diff --git a/articles/data_analysis_omics_using_the_structtoolbox_files/figure-html/unnamed-chunk-61-1.png b/articles/data_analysis_omics_using_the_structtoolbox_files/figure-html/unnamed-chunk-61-1.png
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