DAVIDGODag-methods: Methods for 'DAVIDGODag' class object

In RDAVIDWebService: An R Package for retrieving data from DAVID into R objects using Web Services API.

Description

Obtain DAVIDGODag related information, according to the given function call (see Values).

Usage

  terms(x, ...)

  ## S4 method for signature 'DAVIDGODag'
terms(x, ...)

  percentages(object)

  ## S4 method for signature 'DAVIDGODag'
percentages(object)

  listTotals(object)

  ## S4 method for signature 'DAVIDGODag'
listTotals(object)

  popHits(object)

  ## S4 method for signature 'DAVIDGODag'
popHits(object)

  popTotals(object)

  ## S4 method for signature 'DAVIDGODag'
popTotals(object)

  foldEnrichments(object)

  ## S4 method for signature 'DAVIDGODag'
foldEnrichments(object)

  bonferronis(object)

  ## S4 method for signature 'DAVIDGODag'
bonferronis(object)

  benjaminis(object)

  ## S4 method for signature 'DAVIDGODag'
benjaminis(object)

  fdrs(object)

  ## S4 method for signature 'DAVIDGODag'
fdrs(object)

  counts(object, ...)

  ## S4 method for signature 'DAVIDGODag'
counts(object, ...)

  upsideDown(graph)

  ## S4 method for signature 'graph'
upsideDown(graph)

  ## S4 method for signature 'DAVIDGODag'
universeCounts(r)

  ## S4 method for signature 'DAVIDGODag'
universeMappedCount(r)

Arguments

object,x,r	DAVIDGODag class object.
graph	a graph object with the GO DAG structure.
...	Additional parameters (if required).

Value

according to the call one of the following objects can be returned

upsideDown	the same graph but the arcs with its directions in the other way around. Hence, plot layout would make upside down the graph.
universeMappedCount, universeCounts, counts	modifications to the corresponding GOstats/Category library functions, to keep the same behavior for DAVIDGODag objects.
fdrs, benjaminis, bonferronis	Adjusted method specific p-values for the corresponding nodes/terms.
terms	character vector with GO node names.
popTotals, popHits, listTotals	integer vector with the number of ids, to use in the EASE score calculations, when building the 2x2 contingency table.
percentages	numeric vector with the percentage of the gene list ids present in the term.
foldEnrichments	numeric vector with the ratio of the two proportions for each node/term. For example, if 40/400 (i.e. 10%) of your input genes involved in "kinase activity" and the background information is 300/30000 genes (i.e. 1%) associating with "kinase activity", roughly 10%/1%=10 fold enrichment.

Author(s)

Cristobal Fresno and Elmer A Fernandez

See Also

Other DAVIDGODag: DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDGODag, DAVIDGODag, DAVIDGODag-class, DAVIDGeneCluster, DAVIDGeneCluster, DAVIDGenes, DAVIDGenes, DAVIDGenes, DAVIDTermCluster, DAVIDTermCluster, as, as, as, initialize, initialize, initialize, initialize, initialize, initialize, initialize, summary, summary, summary, summary

Examples

{
##Load the Functional Annotation Chart file report for the input demo
##file 2, using data function. Then, create a DAVIDGODag object using
##Molecular Function main category of DAVIDFunctionalAnnotationChart object,
##obtained from the loaded data.frame funChart2. In addition, we have
##selected a threshold pvalue of 0.001 and removed unattached nodes, in case
##DAVID/GO.db database are not using the same version.
data(funChart2)
davidGODag<-DAVIDGODag(DAVIDFunctionalAnnotationChart(funChart2), type="MF",
pvalueCutoff=0.001, removeUnattached=TRUE)

##Now, we can inspect the enrichment GO DAG using GOstats functionalities:
##counts, pvalues, sigCategories, universeCounts, geneMappedCount, etc.
##However, oddsRatios, expectedCounts and universeMappedCount are not
##available because these results are not available on DAVID's Functional
##Annotation Chart report. In addition geneIdUniverse are not the ones of
##the universe but the ids on the category (geneIdsByCategory).
davidGODag
counts(davidGODag)
pvalues(davidGODag)
sigCategories(davidGODag, p=0.0001)
universeCounts(davidGODag)
geneMappedCount(davidGODag)
geneIdsByCategory(davidGODag)
summary(davidGODag)

##In addition, the new nodeData attributes (term, listTotal, popHit,
##popTotal, foldEnrichment, bonferroni, benjamini, fdr) can be retrieved.
terms(davidGODag)
listTotals(davidGODag)
popHits(davidGODag)
popTotals(davidGODag)
foldEnrichments(davidGODag)
bonferronis(davidGODag)
benjaminis(davidGODag)
fdrs(davidGODag)
}

Example output

Loading required package: graph
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, cbind, colMeans, colSums, colnames, 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: GOstats
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: Category
Loading required package: stats4
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand



Attaching package: 'GOstats'

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

    makeGOGraph

Loading required package: ggplot2

Attaching package: 'RDAVIDWebService'

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

    species

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

    members

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

    counts, species

  GO:0005515   GO:0003700   GO:0043565   GO:0016301   GO:0016772   GO:0005488 
2.369353e-07 6.850590e-03 1.882373e-02 2.614014e-02 2.639663e-01 4.673151e-01 
  GO:0005125   GO:0008083   GO:0005102   GO:0016740   GO:0003677   GO:0001071 
5.881964e-01 1.323223e+00 1.737410e+00 2.869855e+01 3.124026e+01           NA 
  GO:0003674   GO:0003676   GO:0003824   GO:0097159   GO:1901363 
          NA           NA           NA           NA           NA 
Warning message:
system call failed: Cannot allocate memory 

RDAVIDWebService documentation built on Nov. 8, 2020, 8:05 p.m.