GOFrame: GOFrame and GOAllFrame 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 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)

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: 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

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