library(devtools) library(tibble) library(plotly) library(stringr)

devtools::install_github("MassDynamics/MassExpression")

library(MassExpression) utils::packageVersion("MassExpression") #> [1] '0.0.78'

data(package="MassExpression")

intensities <- mq_lfq_data$intensities design <- mq_lfq_data$design parameters <- mq_lfq_data$parameters normalisation_method <- parameters[parameters[,1] == "UseNormalisationMethod",2] species <- parameters[parameters[,1] == "Species",2] labellingMethod <- parameters[parameters[,1] == "LabellingMethod",2] results <- runGenericDiscovery(experimentDesign = design, proteinIntensities = intensities, normalisationMethod = normalisation_method, species = species, labellingMethod = labellingMethod) IntensityExperiment <- results$IntensityExperiment CompleteIntensityExperiment <- results$CompleteIntensityExperiment longIntensityDT <- results$longIntensityDT design <- colData(CompleteIntensityExperiment)

tools::buildVignettes(dir = ".", tangle=TRUE)

output_folder <- "path/to/output/folder" saveOutput(IntensityExperiment = IntensityExperiment, CompleteIntensityExperiment = CompleteIntensityExperiment, longIntensityDT = longIntensityDT, outputFolder = output_folder)

# Render and save QC report  qc_report <- system.file("rmd","QC_report.Rmd", package = "MassExpression") rmarkdown::render(qc_report, params = list(listInt = results, experiment = "Mass Dynamics QC report", output_figure = file.path(output_folder, "figure_html/"), format = "html"), output_file = file.path(output_folder, "QC_Report.html"), output_format=rmarkdown::html_document( self_contained=FALSE, lib_dir=file.path(output_folder,"qc_report_files"), code_folding= "hide", theme="united", toc = TRUE, toc_float = TRUE, fig_caption= TRUE, df_print="paged")) # Render PDF rmarkdown::render(qc_report, params = list(listInt = results, experiment = "Mass Dynamics QC report", output_figure = file.path(output_folder_pdf, "figure_pdf/"), format = "pdf"), output_file = file.path(output_folder_pdf, "QC_Report.pdf"), output_format=rmarkdown::pdf_document( toc = TRUE, fig_caption= TRUE))

sessionInfo() #> R version 4.1.0 (2021-05-18) #> 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.dylib #> LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib #>  #> locale: #> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 #>  #> attached base packages: #> [1] stats4 parallel stats graphics grDevices utils datasets  #> [8] methods base  #>  #> other attached packages: #> [1] MassExpression_0.0.78 SummarizedExperiment_1.22.0 #> [3] GenomicRanges_1.44.0 GenomeInfoDb_1.28.4  #> [5] IRanges_2.26.0 S4Vectors_0.30.2  #> [7] MatrixGenerics_1.4.3 matrixStats_0.61.0  #> [9] Biobase_2.52.0 BiocGenerics_0.38.0  #>  #> loaded via a namespace (and not attached): #> [1] tidyselect_1.1.2 xfun_0.29 purrr_0.3.4  #> [4] lattice_0.20-45 colorspace_2.0-2 vctrs_0.3.8  #> [7] generics_0.1.2 htmltools_0.5.2 yaml_2.2.2  #> [10] utf8_1.2.2 rlang_1.0.1 pillar_1.7.0  #> [13] glue_1.6.2 DBI_1.1.2 RColorBrewer_1.1-2  #> [16] uuid_1.0-3 GenomeInfoDbData_1.2.6 foreach_1.5.2  #> [19] lifecycle_1.0.1 stringr_1.4.0 zlibbioc_1.38.0  #> [22] munsell_0.5.0 gtable_0.3.0 codetools_0.2-18  #> [25] evaluate_0.14 knitr_1.37 fastmap_1.1.0  #> [28] fansi_1.0.2 scales_1.1.1 limma_3.48.3  #> [31] DelayedArray_0.18.0 jsonlite_1.8.0 XVector_0.32.0  #> [34] ggplot2_3.3.5 digest_0.6.29 stringi_1.7.6  #> [37] dplyr_1.0.8 grid_4.1.0 cli_3.2.0  #> [40] tools_4.1.0 bitops_1.0-7 magrittr_2.0.2  #> [43] RCurl_1.98-1.6 tibble_3.1.6 tidyr_1.2.0  #> [46] crayon_1.5.0 pkgconfig_2.0.3 pheatmap_1.0.12  #> [49] ellipsis_0.3.2 Matrix_1.4-0 data.table_1.14.2  #> [52] assertthat_0.2.1 rmarkdown_2.11 rstudioapi_0.13  #> [55] iterators_1.0.14 R6_2.5.1 compiler_4.1.0