## ----ASICSload----------------------------------------------------------- library(ASICS) library(ASICSdata) ## ----lib----------------------------------------------------------------- head(getSampleName(pure_library), n = 8) ## ----import_create_lib, results='hide'----------------------------------- pure_spectra <- importSpectraBruker(system.file("extdata", "example_library", package = "ASICS")) new_pure_library <- createPureLibrary(pure_spectra, nb.protons = c(5, 4)) ## ----select_merge_lib---------------------------------------------------- merged_pure_library <- c(pure_library[1:10], new_pure_library) ## ----import_from_Bruker, results='hide'---------------------------------- spectra_data <- importSpectraBruker(system.file("extdata", "Human_diabetes_example", package = "ASICSdata")) ## ----import_from_txt, results='hide'------------------------------------- diabetes <- system.file("extdata", "spectra_diabetes_example.txt", package = "ASICSdata") spectra_data_txt <- read.table(diabetes, header = TRUE, row.names = 1) ## ----preprocessing, results='hide'--------------------------------------- spectra_base_cor <- baselineCorrection(spectra_data_txt) ## ----create_spectra, results='hide'-------------------------------------- spectra_obj <- createSpectra(spectra_base_cor) ## ----ASICS, results='hide'----------------------------------------------- # part of the spectrum to exclude (water and urea) to_exclude <- matrix(c(4.5, 5.1, 5.5, 6.5), ncol = 2, byrow = TRUE) ASICS_results <- ASICS(spectra_obj, exclusion.areas = to_exclude) ## ----summary_res--------------------------------------------------------- ASICS_results ## ----plot_spectrum, warning=FALSE, fig.width=12, fig.height=8------------ plot(ASICS_results, idx = 1, xlim = c(2.8, 3.3), add.metab = "Creatinine") ## ----rel_conc------------------------------------------------------------ head(getQuantification(ASICS_results), 10)[, 1:2] ## ----design-------------------------------------------------------------- design <- read.table(system.file("extdata", "design_diabete_example.txt", package = "ASICSdata"), header = TRUE) ## ----analyses_obj-------------------------------------------------------- analysis_data <- formatForAnalysis(getQuantification(ASICS_results), design = design, zero.threshold = 75, zero.group = "condition", outliers = c("ADG10003u_007", "ADG19007u_163")) ## ----pca, fig.width=10--------------------------------------------------- resPCA <- pca(analysis_data) plot(resPCA, graph = "ind", col.ind = "condition") plot(resPCA, graph = "var") ## ----oplsda-------------------------------------------------------------- resOPLSDA <- oplsda(analysis_data, condition = "condition", orthoI = 1) resOPLSDA ## ----oplsda_plot, fig.width=10, results='hide'--------------------------- plot(resOPLSDA) ## ----perform_tests------------------------------------------------------- resTests <- kruskalWallis(analysis_data, "condition") resTests ## ----test_plot, fig.width=10, fig.height=10, results='hide'-------------- plot(resTests) ## ----align_and_binning, results='hide'----------------------------------- spectra_align <- alignment(spectra_data_txt) spectra_bucket <- binning(spectra_align) ## ----create_ana_obj------------------------------------------------------ analysis_data_bucket <- formatForAnalysis(spectra_bucket, design = design, zero.threshold = 75) ## ----oplsda_buckets------------------------------------------------------ resOPLSDA_buckets <- oplsda(analysis_data_bucket, condition = "condition", type.data = "buckets") resOPLSDA_buckets ## ----oplsda_buckets_plot, fig.width=10----------------------------------- plot(resOPLSDA_buckets, graph = "buckets") ## ----sysinfo------------------------------------------------------------- sessionInfo()