annotate {Onassis} | R Documentation |
annotate
This method annotates the entities contained in a data frame with the concepts from a specific dictionary.
annotate(input = NA, dictType = NA, dictionary = NA, ...) ## S4 method for signature 'data.frame,character,character' annotate(input, dictType = "OBO", dictionary = NA, dictoutdir = getwd(), d_synonymtype = "EXACT", taxID = 0, annot_out = getwd(), paramValueIndex = NA, SearchStrategy = "CONTIGUOUS_MATCH", CaseMatch = "CASE_INSENSITIVE", Stemmer = "NONE", StopWords = "NONE", OrderIndependentLookup = "ON", FindAllMatches = "YES", e_synonymtype = "ALL", multipleDocs = FALSE, disease = FALSE)
input |
A data frame where the first column is the ID of the sample or document to annotate |
dictType |
the type of input dictionary
|
dictionary |
The local OBO/OWL ontology to be converted into an XML Conceptmapper dictionary or the URL to download the file. If NA is passed and the |
... |
Optional parameters |
dictoutdir |
Optional parameter to specify the location where the Conceptmapper dictionary file will be stored. Defaults to current working directory. |
d_synonymtype |
Optional parameter to specify the type of synonyms to consider when building the dictionary for Conceptmapper. For further detail http://owlcollab.github.io/oboformat/doc/obo-syntax.html. Default: EXACT
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taxID |
the taxonomy identifier of the organism when the |
annot_out |
The path of the output directory where Conceptmapper annotation files will be stored |
paramValueIndex |
An integer value to index the 576 parameter combinations |
SearchStrategy |
The matching strategy for finding concepts in the input text
|
CaseMatch |
|
Stemmer |
|
StopWords |
|
OrderIndependentLookup |
|
FindAllMatches |
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e_synonymtype |
The type of synoyms for the EntityFinder
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multipleDocs |
TRUE when multiple documents are loaded from a single file with each row representing a document. The file should have two columns. The first for the unique document identifier and the second for the textual descriptions |
disease |
A logical value set to TRUE if the annotation requires the 'Healthy' condition to be found. |
instance of class Onassis-class
with annotated entities
geo_chip <- readRDS(system.file('extdata', 'vignette_data', 'GEO_human_chip.rds', package='Onassis')) obo <- system.file('extdata', 'sample.cs.obo', package='OnassisJavaLibs') onassis_results <- annotate(geo_chip, 'OBO', dictionary=obo) entities <- entities(onassis_results) entities <- entities[sample(nrow(entities), 30),]