## ----echo = FALSE,include=FALSE-----------------------------------------------
suppressPackageStartupMessages(library(metabolomicsWorkbenchR))
library(structToolbox)

## -----------------------------------------------------------------------------
names(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)

## -----------------------------------------------------------------------------
DE = do_query(
  context = 'study',
  input_item = 'analysis_id',
  input_value = 'AN000025',
  output_item = 'untarg_DatasetExperiment'
)
DE


## -----------------------------------------------------------------------------
# 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)])