## ----echo = FALSE,include=FALSE----------------------------------------------- suppressPackageStartupMessages(library(grid)) suppressPackageStartupMessages(library(httptest)) suppressPackageStartupMessages(library(metabolomicsWorkbenchR)) httptest::start_vignette('introduction') ## ----------------------------------------------------------------------------- # search for all studies with "Diabetes" in the title and return a summary df = do_query( context = 'study', input_item = 'study_title', input_value = 'Diabetes', output_item = 'summary' ) df[1:3,c(1,4)] ## ----------------------------------------------------------------------------- df = do_query( context = 'compound', input_item = 'regno', input_value = '11', output_item = 'compound_exact' ) df[,1:3] ## ----eval=FALSE--------------------------------------------------------------- # img = do_query( # context = 'compound', # input_item = 'regno', # input_value = '11', # output_item = 'png' # ) # # grid.raster(img) # ## ----------------------------------------------------------------------------- # valid contexts names(context) # context, input_item or output_item ## ----------------------------------------------------------------------------- # valid inputs for "study" context context_inputs('study') ## ----------------------------------------------------------------------------- df = do_query( context = 'study', input_item = 'ignored', input_value = 'ignored', output_item = 'untarg_studies' ) df[1:3,1:3] ## ----------------------------------------------------------------------------- df = do_query( context = 'compound', input_item = 'regno', input_value = '11', output_item = 'compound_exact' ) df[,1:3] ## ----------------------------------------------------------------------------- df = do_query( context = 'gene', input_item = 'gene_name', input_value = 'acetyl-CoA', output_item = 'gene_partial' ) df[1:3,1:3] ## ----------------------------------------------------------------------------- SE = do_query( context = 'study', input_item = 'study_id', input_value = 'ST000001', output_item = 'SummarizedExperiment' # or 'DatasetExperiment' ) SE ## ----------------------------------------------------------------------------- MAE = do_query( context = 'study', input_item = 'study_id', input_value = 'ST000009', output_item = 'MultiAssayExperiment' ) MAE ## ----eval=FALSE--------------------------------------------------------------- # SE = do_query( # context = 'study', # input_item = 'analysis_id', # input_value = 'AN000025', # output_item = 'untarg_SummarizedExperiment' # or 'untarg_DatasetExperiment' # ) # # SE ## ----eval=TRUE,include=FALSE,echo=TRUE---------------------------------------- SE = metabolomicsWorkbenchR:::AN000025 ## ----------------------------------------------------------------------------- # list all context names names(metabolomicsWorkbenchR::context) ## ----------------------------------------------------------------------------- # list valid inputs/outputs for the "study" context metabolomicsWorkbenchR::context$study ## ----------------------------------------------------------------------------- # input item "study_id" info input_item$study_id ## ----------------------------------------------------------------------------- # output item 'summary' info output_item$summary ## ----echo=FALSE--------------------------------------------------------------- sessionInfo() ## ----include=FALSE------------------------------------------------------------ end_vignette()