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string search of concepts by name in the CONCEPT_RELATIONSHIP table

Source: R/omop_relations_names.R
omop_relations_names.Rd

a different (and quicker) way of finding relationships than omop_relations() that gets relations of a specified concept note that names are not contained in CONCEPT_RELATIONSHIP so the function joins to CONCEPT to query

Usage

omop_relations_names(
  findstring,
  ignore_case = TRUE,
  exact = FALSE,
  fixed = FALSE,
  c_ids = NULL,
  d_ids = NULL,
  v_ids = NULL,
  cc_ids = NULL,
  standard = NULL,
  messages = TRUE
)

ornames(
  findstring,
  ignore_case = TRUE,
  exact = FALSE,
  fixed = FALSE,
  c_ids = NULL,
  d_ids = NULL,
  v_ids = NULL,
  cc_ids = NULL,
  standard = NULL,
  messages = TRUE
)

Arguments

findstring

to search for or regex, e.g. "^a" to find those starting with A

ignore_case

ignore case in string comparison, default TRUE

exact

TRUE for exact string search, "start" for exact start, "end" for exact end, default=FALSE for str_detect

fixed

default FALSE allows regex,TRUE uses grepl exact matching

c_ids

one or more concept_id to filter by, default NULL for all

d_ids

one or more domain_id to filter by, default NULL for all

v_ids

one or more vocabulary_id to filter by, default NULL for all

cc_ids

one or more concept_class_id to filter by, default NULL for all

standard

one or more standard_concept to filter by, default NULL for all, S,C

messages

whether to print info messages, default=TRUE

Examples

#1 min to return 38 concepts
orn <- omop_relations_names("diffuse large B cell lymphoma")
#> returning 38 concepts
#omop_relations_names("AJCC/UICC Stage")
#omop_relations_names("chemotherapy", v_ids="LOINC")
#omop_relations_names("chemotherapy", v_ids=c("LOINC","SNOMED"), d_ids=c("Observation","Procedure"))
#set the findstring to "" to get all rows satisfying the other conditions
#omop_relations_names("", v_ids="Gender")
#omop_relations_names("", d_ids="Type Concept", standard="S")