KEGGFrame: KEGGFrame objects

In AnnotationDbi: Manipulation of SQLite-based annotations in Bioconductor

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)

Example output

Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required namespace: KEGG.db

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

  KEGGIds genes
1   04610     2
2   00232     9
3   00983     9
4   00232    10

AnnotationDbi documentation built on Nov. 8, 2020, 4:50 p.m.