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.
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.
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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: GO.db There were 25 warnings (use warnings() to see them) go_id evidence gene_id 1 GO:0001666 IDA 100 2 GO:0006950 IDA 100 3 GO:0008150 IDA 100 4 GO:0008150 IEA 10 5 GO:0008150 ND 1 6 GO:0008152 IEA 10 7 GO:0009628 IDA 100 8 GO:0036293 IDA 100 9 GO:0050896 IDA 100 10 GO:0070482 IDA 100
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