Genomics API

Function to search expression matrix, proteomics matrix, CNV matrix; allows slicing across multiple dimensions. However measurementset (i.e. pipeline) must be supplied (currently allows searching one pipeline at a time)

search_expression(
  measurementset = NULL,
  biosample = NULL,
  feature = NULL,
  formExpressionSet = TRUE,
  featureNameAsFeatureIdentifier = TRUE,
  biosample_ref = NULL,
  con = NULL
)

`measurementset`	(Mandatory) dataframe containing pipeline information; typically output of a `get_measurementsets(measurementset_id = ...)` or `search_measurementsets(dataset_id = ..)` call
`biosample`	(Optional) dataframe containing biosample information; typically output of a `search_biosamples(dataset_id = ..)` call. If not specified, function returns all biosamples available by other search parameters
`feature`	(Optional) dataframe containing feature information; typically output of a `search_features(gene_symbol = ...)` call. If not specified, function returns all features available by other search parameters
`formExpressionSet`	(default: TRUE) whether to return result as a Bioconductor ExpressionSet object
`featureNameAsFeatureIdentifier`	(default: TRUE) whether to use FEATURE.name or FEATURE.gene_symnbol as rowname of ExpressionSet object
`biosample_ref`	(Optional) data-frame containing all biosamples in a study, i.e. typically output of `search_biosamples(dataset_id = ..)` call, or all biosamples available to logged in user, i.e. output of `get_biosamples(biosample_id = NULL)`. When not searching by `biosample`, and when requesting to return an ExpressionSet object, supplying this parameter can optimize function exection time because function does not have to do biosample lookup internally
`con`	(Optional) database connection object; typically output of `rg_connect2()` call. If not specified, connection object is formulated from internally stored values of `rg_connect()` call