addComposeLookupToCDB: Add composition lookups to CDB

In anoopshah/Rdiagnosislist: Manipulate SNOMED CT Diagnosis Lists

Add composition lookups to CDB

Description

Creates a composition lookup table for a set of SNOMED CT concepts based on output of ‘decompose’, and adds it to the CDB

Usage

addComposeLookupToCDB(
  decompositions,
  CDB,
  maxcol = 10,
  SNOMED = getSNOMED(),
  ...
)

Arguments

decompositions	vector of filenames of decompose output (read by fread) or data.frame containing outputs of decompose function
CDB	concept database environment, containing a table called FINDINGS
maxcol	maximum number of attributes columns. If NULL it is determined from the data. It might be helpful to specify it so that downstream databases and programs know exactly how many columns to expect. We suggest setting it to 10 which should handle all possible SNOMED CT concept decompositions.
SNOMED	environment containing a SNOMED CT dictionary
...	other arguments to pass to fread

Value

CDB environment with an additional data.table ‘COMPOSELOOKUP’ with columns rootId, attr_1 ... attr_X (up to maxcol), with, due_to, without, origId (all with data type integer64 and class 'SNOMEDconcept')

See Also

decompose, compose, batchDecompose

Other CDB functions: addWordnet(), batchDecompose(), createCDB(), downloadOrphanet(), downloadWordnet()

anoopshah/Rdiagnosislist documentation built on March 29, 2025, 10:46 a.m.