Genomics API

Register entities using list of R data-frames list of R data-frames has complete data about metadata (PROJECT, DATASET, INDIVIDUAL, ...) , and links to files storing the MeasurementData entities (e.g. RNASeq, Variant etc.)

register_entities_workbook(
  workbook,
  register_upto_entity = c("all", "DEFINITION", "INDIVIDUAL", "BIOSAMPLE",
    "MEASUREMENTSET", "MEASUREMENT"),
  entity_to_update = c(NULL, "PROJECT", "DATASET", "INDIVIDUAL", "BIOSAMPLE",
    "EXPERIMENTSET", "MEASUREMENTSET", "all"),
  register_measurement_entity = c("all", "RNAQUANTIFICATION",
    "RNAQUANTIFICATION_STRING", "VARIANT", "FUSION", "PROTEOMICS", "COPYNUMBER_MAT",
    "COPYNUMBER_MAT_STRING", "COPYNUMBER_VARIANT", "CYTOMETRY_CYTOF", "MEASUREMENT"),
  reader_config = yaml.load_file(system.file("extdata", "datareader_config.yaml",
    package = "revealgenomics")),
  loader_config = yaml.load_file(system.file("extdata", "dataloader_config.yaml",
    package = "revealgenomics")),
  permissions_config = get_revealgenomics_config(),
  pipeline_name_filter = NULL,
  con = NULL
)

`register_upto_entity`	use this parameter to restrict load up to an user-specified entity. e.g. you can load up to the following and not load the rest: (1) `DEFINITION` (this includes `PROJECT` and `DATASET`), or (2) `INDIVIDUAL`, and so on. The ordering is same as in the parameter definition below. Default value is `all` i.e. all entities are loaded
`entity_to_update`	enable excel sheet loader to update one entity at a time - applies to project, dataset, individual, biosample, experimentset, measurementset. If `all` is supplied, then all metadata entities will be updated
`register_measurement_entity`	use this parameter to restrict which measurement-data types should be loaded by the function. Default value is `all` i.e. all measurement-types are loaded
`reader_config`	YAML object storing mappings from `pipeline+filter` strings to specific `DataReader`-s. Default: read from `datareader_config.yaml` at `inst/extdata/` location of `revealgenomics` package
`loader_config`	YAML object storing mappings from `pipeline+filter` strings to specific `DataLoader`-s. Default: read from `dataloader_config.yaml` at `inst/extdata/` location of `revealgenomics` package
`permissions_config`	YAML object storing list of users that will be automatically granted access to studies being loaded. If not supplied by user, config is read via `get_revealgenomics_config` function `get_revealgenomics_config()` from file `/etc/revealgenomics_config.yaml`. Visit `inst/extdata/revealgenomics_config_sample.yaml` to see example config file
`pipeline_name_filter`	use this filter to restrict data-loading to pipelines with fully/partially matched names. Default value is `NULL` (i.e. no checking by name done)