View source: R/api_excel_loader.R
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.)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | 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) |
entity_to_update |
enable excel sheet loader to update one entity at a time
- applies to project, dataset, individual, biosample, experimentset,
measurementset. If |
register_measurement_entity |
use this parameter to restrict which measurement-data types
should be loaded by the function.
Default value is |
reader_config |
YAML object storing mappings from |
loader_config |
YAML object storing mappings from |
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 |
pipeline_name_filter |
use this filter to restrict data-loading to pipelines with fully/partially
matched names. Default value is |
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