export_annotations {ontoFAST}

Export annotation data

Description

This function converts character annotations stored in shiny_in object to table format.

Usage

export_annotations(
  ontology,
  annotations = "auto",
  incl.names = FALSE,
  sep.head = ", ",
  sep.tail = NULL,
  collapse = NULL
)

Arguments

ontology

Ontology

annotations

which annotations to use: "auto" means automatic annotations, "manual" means manual ones. Alternatively, any othe list element containing annotations can be specified.

incl.names

if TRUE includes terms' names and IDs, otherwise includes just IDs.

sep.head

if incl.names=TRUE, this is a separator attached to the begining of term's ID

sep.tail

if incl.names=TRUE, this is a separator attached to the end of term's ID

collapse

if NULL all annotations of a term placed in separate columns, if a value is specified (e.g., "; ") then all anotations are collapsed in one line given that values

Value

Returns a table

Examples

data(Sharkey_2011)
data(HAO)
hao_obo<-onto_process(HAO, Sharkey_2011[,1], do.annot = FALSE)
ontofast <- new.env(parent = emptyenv())
ontofast$shiny_in <- make_shiny_in(hao_obo)
# runOntoFast(is_a = c("is_a"), part_of = c("BFO:0000050"), shiny_in="shiny_in" )
tb<-export_annotations(ontofast$shiny_in, annotations="manual", incl.names=TRUE,collapse="; ")
tb<-export_annotations(ontofast$shiny_in, annotations="auto", incl.names=TRUE,collapse="; ")
tb<-export_annotations(ontofast$shiny_in, annotations="auto", incl.names=TRUE,collapse=NULL)
# save annotations in csv
# write.csv(tb, "annotated_characters.csv")