diff --git a/vignettes/global_LFQ_prot_tutorial.Rmd b/vignettes/global_LFQ_prot_tutorial.Rmd new file mode 100644 index 0000000..c761763 --- /dev/null +++ b/vignettes/global_LFQ_prot_tutorial.Rmd @@ -0,0 +1,63 @@ +--- +title: "FragPipeAnalystR LFQ tutorial" +output: + html_document: + keep_md: yes +--- + +# Introduction + +Here we presented the usage of FragPipeAnalystR to reproduce AP-MS analysis previously demonstrated in the manuscript. Note that in the manuscript, we used the FragPipeAnalyst website, but you could reproduce the same analysis with FragPipeR. + +## Reading input files +``` {r include=T, warning=F} +library(FragPipeAnalystR) +se <- make_se_from_files("/Users/hsiaoyi/Documents/workspace/FragPipeR_manuscript/data/AP-MS/combined_protein.tsv", + "/Users/hsiaoyi/Documents/workspace/FragPipeR_manuscript/data/AP-MS/experiment_annotation.tsv", + type = "LFQ", level = "protein") +``` + +``` {r include=T, warning=F} +plot_pca(se) +``` + +``` {r include=T, warning=F} +plot_correlation_heatmap(se) +``` + +``` {r include=T, warning=F} +plot_missval_heatmap(se) +``` + +``` {r include=T, warning=F} +plot_feature_numbers(se) +``` + +```{r include=T, warning=F} +colData(se)$condition +``` + +## Imputation +```{r include=T, warning=F} +imputed_se <- manual_impute(se) +``` + + +``` {r include=T, warning=F} +plot_pca(imputed_se) +``` + +``` {r include=T, warning=F} +plot_correlation_heatmap(imputed_se) +``` + +## Differential expression analysis +```{r include=T, warning=F} +de_result <- test_limma(imputed_se, type = "all") +de_result_updated <- add_rejections(de_result) +plot_volcano(de_result_updated, "CCND1_vs_CONTROL") +``` + +``` {r include=T, warning=F} +sessionInfo() +``` diff --git a/vignettes/global_LFQ_prot_tutorial.md b/vignettes/global_LFQ_prot_tutorial.md new file mode 100644 index 0000000..b3a2d11 --- /dev/null +++ b/vignettes/global_LFQ_prot_tutorial.md @@ -0,0 +1,186 @@ +--- +title: "FragPipeAnalystR LFQ tutorial" +output: + html_document: + keep_md: yes +--- + +# Introduction + +Here we presented the usage of FragPipeAnalystR to reproduce AP-MS analysis previously demonstrated in the manuscript. Note that in the manuscript, we used the FragPipeAnalyst website, but you could reproduce the same analysis with FragPipeR. + +## Reading input files + +```r +library(FragPipeAnalystR) +se <- make_se_from_files("/Users/hsiaoyi/Documents/workspace/FragPipeR_manuscript/data/AP-MS/combined_protein.tsv", + "/Users/hsiaoyi/Documents/workspace/FragPipeR_manuscript/data/AP-MS/experiment_annotation.tsv", + type = "LFQ", level = "protein") +``` + + +```r +plot_pca(se) +``` + +![](global_LFQ_prot_tutorial_files/figure-html/unnamed-chunk-2-1.png) + + +```r +plot_correlation_heatmap(se) +``` + +![](global_LFQ_prot_tutorial_files/figure-html/unnamed-chunk-3-1.png) + + +```r +plot_missval_heatmap(se) +``` + +![](global_LFQ_prot_tutorial_files/figure-html/unnamed-chunk-4-1.png) + + +```r +plot_feature_numbers(se) +``` + +![](global_LFQ_prot_tutorial_files/figure-html/unnamed-chunk-5-1.png) + + +```r +colData(se)$condition +``` + +``` +## [1] "CCND1" "CCND1" "CCND1" "CONTROL" "CONTROL" "CONTROL" "CONTROL" +``` + +## Imputation + +```r +imputed_se <- manual_impute(se) +``` + + + +```r +plot_pca(imputed_se) +``` + +![](global_LFQ_prot_tutorial_files/figure-html/unnamed-chunk-8-1.png) + + +```r +plot_correlation_heatmap(imputed_se) +``` + +![](global_LFQ_prot_tutorial_files/figure-html/unnamed-chunk-9-1.png) + +## Differential expression analysis + +```r +de_result <- test_limma(imputed_se, type = "all") +``` + +``` +## Tested contrasts: CCND1_vs_CONTROL +``` + +```r +de_result_updated <- add_rejections(de_result) +plot_volcano(de_result_updated, "CCND1_vs_CONTROL") +``` + +![](global_LFQ_prot_tutorial_files/figure-html/unnamed-chunk-10-1.png) + + +```r +sessionInfo() +``` + +``` +## R version 4.3.1 Patched (2023-10-12 r85331) +## Platform: aarch64-apple-darwin20 (64-bit) +## Running under: macOS Ventura 13.4 +## +## Matrix products: default +## BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib +## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 +## +## locale: +## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 +## +## time zone: America/Detroit +## tzcode source: internal +## +## attached base packages: +## [1] stats graphics grDevices datasets utils methods base +## +## other attached packages: +## [1] FragPipeAnalystR_0.1.4 +## +## loaded via a namespace (and not attached): +## [1] bitops_1.0-7 fdrtool_1.2.17 +## [3] rlang_1.1.3 magrittr_2.0.3 +## [5] clue_0.3-65 GetoptLong_1.0.5 +## [7] matrixStats_1.3.0 compiler_4.3.1 +## [9] png_0.1-8 vctrs_0.6.5 +## [11] stringr_1.5.1 ProtGenerics_1.34.0 +## [13] pkgconfig_2.0.3 shape_1.4.6.1 +## [15] crayon_1.5.2 fastmap_1.1.1 +## [17] XVector_0.42.0 labeling_0.4.3 +## [19] utf8_1.2.4 rmarkdown_2.26 +## [21] tzdb_0.4.0 preprocessCore_1.64.0 +## [23] purrr_1.0.2 xfun_0.43 +## [25] zlibbioc_1.48.2 cachem_1.0.8 +## [27] SNFtool_2.3.1 GenomeInfoDb_1.38.8 +## [29] jsonlite_1.8.8 ExPosition_2.8.23 +## [31] highr_0.10 DelayedArray_0.28.0 +## [33] BiocParallel_1.36.0 parallel_4.3.1 +## [35] cluster_2.1.4 R6_2.5.1 +## [37] stringi_1.8.3 bslib_0.7.0 +## [39] RColorBrewer_1.1-3 limma_3.58.1 +## [41] GenomicRanges_1.54.1 jquerylib_0.1.4 +## [43] assertthat_0.2.1 Rcpp_1.0.12 +## [45] SummarizedExperiment_1.32.0 iterators_1.0.14 +## [47] knitr_1.46 readr_2.1.5 +## [49] flowCore_2.14.2 IRanges_2.36.0 +## [51] Matrix_1.6-1.1 tidyselect_1.2.1 +## [53] rstudioapi_0.16.0 abind_1.4-5 +## [55] yaml_2.3.8 doParallel_1.0.17 +## [57] codetools_0.2-19 affy_1.80.0 +## [59] lattice_0.21-9 tibble_3.2.1 +## [61] plyr_1.8.9 withr_3.0.0 +## [63] Biobase_2.62.0 evaluate_0.23 +## [65] ConsensusClusterPlus_1.66.0 circlize_0.4.16 +## [67] pillar_1.9.0 affyio_1.72.0 +## [69] BiocManager_1.30.22 MatrixGenerics_1.14.0 +## [71] renv_0.17.0 foreach_1.5.2 +## [73] stats4_4.3.1 plotly_4.10.4 +## [75] MSnbase_2.28.1 MALDIquant_1.22.2 +## [77] ncdf4_1.22 generics_0.1.3 +## [79] RCurl_1.98-1.14 hms_1.1.3 +## [81] S4Vectors_0.40.2 ggplot2_3.5.1 +## [83] munsell_0.5.1 scales_1.3.0 +## [85] glue_1.7.0 lazyeval_0.2.2 +## [87] tools_4.3.1 data.table_1.15.4 +## [89] mzID_1.40.0 vsn_3.70.0 +## [91] mzR_2.36.0 XML_3.99-0.16.1 +## [93] grid_4.3.1 impute_1.76.0 +## [95] tidyr_1.3.1 RProtoBufLib_2.14.1 +## [97] prettyGraphs_2.1.6 MsCoreUtils_1.14.1 +## [99] colorspace_2.1-0 GenomeInfoDbData_1.2.11 +## [101] cmapR_1.14.0 cli_3.6.2 +## [103] fansi_1.0.6 viridisLite_0.4.2 +## [105] cytolib_2.14.1 S4Arrays_1.2.1 +## [107] ComplexHeatmap_2.18.0 dplyr_1.1.4 +## [109] pcaMethods_1.94.0 gtable_0.3.5 +## [111] sass_0.4.9 digest_0.6.35 +## [113] BiocGenerics_0.48.1 ggrepel_0.9.5 +## [115] SparseArray_1.2.4 farver_2.1.1 +## [117] htmlwidgets_1.6.4 rjson_0.2.21 +## [119] htmltools_0.5.8.1 lifecycle_1.0.4 +## [121] httr_1.4.7 alluvial_0.1-2 +## [123] GlobalOptions_0.1.2 statmod_1.5.0 +## [125] MASS_7.3-60 +``` diff --git 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