register_entities_workbook: register entities via list of R data-frames

Description Usage Arguments

View source: R/api_excel_loader.R

Description

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.)

Usage

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register_entities_workbook(workbook, register_upto_entity = c("all",
  "ONTOLOGY", "DEFINITION", "INDIVIDUAL", "BIOSAMPLE", "MEASUREMENTSET",
  "MEASUREMENT"), entity_to_update = c(NULL, "PROJECT", "DATASET",
  "INDIVIDUAL", "BIOSAMPLE", "EXPERIMENTSET", "MEASUREMENTSET", "all"),
  register_measurement_entity = c("all", "RNAQUANTIFICATION", "VARIANT",
  "FUSION", "PROTEOMICS", "COPYNUMBER_SEG", "COPYNUMBER_MAT"),
  pipeline_name_filter = NULL, con = NULL)

Arguments

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) ONTOLOGY, or (2) DEFINITION (this includes PROJECT and DATASET), or (3) 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

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)


Paradigm4/revealgenomics documentation built on Jan. 17, 2019, 3:53 a.m.