GOFrame: GOFrame and GOAllFrame objects

In jmacdon/AnnotationDbi: Manipulation of SQLite-based annotations in Bioconductor

Description

These objects each contain a data frame which is required to be composed of 3 columns. The 1st column are GO IDs. The second are evidence codes and the 3rd are the gene IDs that match to the GO IDs using those evidence codes. There is also a slot for the organism that these anotations pertain to.

Details

The GOAllFrame object can only be generated from a GOFrame object and its contructor method does this automatically from a GOFrame argument. The purpose of these objects is to create a safe way for annotation data about GO from non-traditional sources to be used for analysis packages like GSEABase and eventually GOstats.

Examples

  ## Make up an example
  genes = c(1,10,100)
  evi = c("ND","IEA","IDA")
  GOIds = c("GO:0008150","GO:0008152","GO:0001666")
  frameData = data.frame(cbind(GOIds,evi,genes))

  library(AnnotationDbi)
  frame=GOFrame(frameData,organism="Homo sapiens")
  allFrame=GOAllFrame(frame)

  getGOFrameData(allFrame)

jmacdon/AnnotationDbi documentation built on Oct. 22, 2021, 9:14 p.m.