get_entity: Query an entity and return the resulting dataframe,...

In Paradigm4/revealcore: SciDB REVEAL Core API

Query an entity and return the resulting dataframe, optionally including info fields

Description

Query an entity and return the resulting dataframe, optionally including info fields

Usage

get_entity(
  con,
  pkg_schema,
  entitynm,
  aop = F,
  include_info_array = F,
  join_info_array = T,
  query_attributes = NULL,
  semi_join_args = NULL,
  ...
)

Arguments

aop	if TRUE, return the arrayop object instead of the data frame. Only possible if not returning an info array
include_info_array	if TRUE, also query the info array for the entity if one exists
join_info_array	if TRUE and using include_info_array, return a single data frame with the info array joined to the main array. Otherwise, return a list of the two dataframes
query_attributes	if TRUE, filtering/joining on attributes of main array. Inferred automatically is using ... parameter, but needs to be set manually if using semi_join_args, particularly is semi_join_args contains any arrayop objects
semi_join_args	an ordered list of things to semi_join the queried array by.
...	If semi_join_args is not provided, can provide items to join on here. ⁠get_entity(*, dataset_id=1:10, dataset_version=1)⁠ is equivalent to ⁠get_entity(*, semi_join_args = list(data.frame(dataset_id=1:10), data.frame(dataset_version=1))⁠

Examples

## Not run: 
gs_query = revealcore:::get_entity(con, revealgenomics:::.ghEnv, "GENE_SYMBOL", gene_symbol=c("BRCA1","BRCA2"), aop = T)
revealcore:::get_entity(con, revealgenomics:::.ghEnv, "FEATURE", semi_join_args=list(data.frame("featureset_id"=1:10), gs_query), include_info_array=T, query_attributes=F)
revealcore:::get_entity(con, revealgenomics:::.ghEnv, "FEATURE", semi_join_args=list(data.frame("featureset_id"=1:10), gs_query, data.frame("feature_type"="gene")), include_info_array=T, query_attributes=T, join_info_array=F)
revealcore:::get_entity(con, revealgenomics:::.ghEnv, "FEATURE", semi_join_args=list(data.frame("featureset_id"=1:10), gs_query, data.frame("feature_type"="gene")), include_info_array=T, query_attributes=T, join_info_array=T)

## End(Not run)

Paradigm4/revealcore documentation built on May 21, 2023, 9:57 a.m.