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.
just an accessor method and returns the data.frame contained in the
KEGGFrame object and is mostly used by other code internally.
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.
1 2 3 4 5 6 7 8 9
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
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