## ----echo = FALSE,include=FALSE----------------------------------------------- suppressPackageStartupMessages(library(structToolbox)) suppressPackageStartupMessages(library(httptest)) suppressPackageStartupMessages(library(metabolomicsWorkbenchR)) httptest::start_vignette('structToolbox_example') ## ----------------------------------------------------------------------------- names(metabolomicsWorkbenchR::context) ## ----------------------------------------------------------------------------- cat('Valid inputs:\n') context_inputs('study') cat('\nValid outputs:\n') context_outputs('study') ## ----------------------------------------------------------------------------- US = do_query( context = 'study', input_item = 'ignored', input_value = 'ignored', output_item = 'untarg_studies' ) head(US[,1:3]) ## ----------------------------------------------------------------------------- S = do_query('study','study_id','ST000010','summary') t(S) ## ----eval=FALSE--------------------------------------------------------------- # DE = do_query( # context = 'study', # input_item = 'analysis_id', # input_value = 'AN000025', # output_item = 'untarg_DatasetExperiment' # ) # DE ## ----eval=TRUE,include=FALSE-------------------------------------------------- DE=metabolomicsWorkbenchR:::AN000025 DE=as.DatasetExperiment(DE) DE ## ----warning=FALSE------------------------------------------------------------ # model sequence M = mv_feature_filter( threshold = 40, method='across', factor_name='FCS') + mv_sample_filter(mv_threshold =40) + vec_norm() + knn_impute() + log_transform() + mean_centre() + PCA() # apply model M = model_apply(M,DE) # pca scores plot C = pca_scores_plot(factor_name=c('FCS')) chart_plot(C,M[length(M)]) ## ----echo=FALSE--------------------------------------------------------------- sessionInfo() ## ----include=FALSE------------------------------------------------------------ end_vignette()