KEGGFrame: KEGGFrame objects

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

KEGGFrame objects

Description

These objects each contain a data frame which is required to be composed of 2 columns. The 1st column are KEGG IDs. The second are the gene IDs that match to the KEGG IDs. There is also a slot for the organism that these anotations pertain to. getKEGGFrameData is just an accessor method and returns the data.frame contained in the KEGGFrame object and is mostly used by other code internally.

Details

The purpose of these objects is to create a safe way for annotation data about KEGG from non-traditional sources to be used for analysis packages like GSEABase and eventually Category.

Examples

  ## Make up an example
  genes = c(2,9,9,10)
  KEGGIds = c("04610","00232","00983","00232")
  frameData = data.frame(cbind(KEGGIds,genes))

  library(AnnotationDbi)
  frame=KEGGFrame(frameData,organism="Homo sapiens")

  getKEGGFrameData(frame)

Bioconductor/AnnotationDbi documentation built on Nov. 2, 2024, 6:27 a.m.