CollectionType-constructors: Collection Type Class Constructors

In GSEABase: Gene set enrichment data structures and methods

Description

These functions construct collection types. Collection types can be used in manipulating (e.g., selecting) sets, and can contain information specific to particular sets (e.g., 'category' and 'subcategory' classifications of 'BroadCollection'.)

Usage

NullCollection(...)
ComputedCollection(...)
ExpressionSetCollection(...)
ChrCollection(ids,...)
ChrlocCollection(ids,...)
KEGGCollection(ids,...)
MapCollection(ids,...)
OMIMCollection(ids,...)
PMIDCollection(ids,...)
PfamCollection(ids, ...)
PrositeCollection(ids, ...)
GOCollection(ids=character(0), evidenceCode="ANY", ontology="ANY", ..., err=FALSE)
OBOCollection(ids, evidenceCode="ANY", ontology="ANY", ...)
BroadCollection(category, subCategory=NA, ...)

Arguments

category	(Required) Broad category, one of "c1" (postitional), "c2" (curated), "c3" (motif), "c4" (computational), "c5" (GO), "c6" (Oncogenic Pathway Activation Modules) "c7" (Immunologic Signatures), "c8" (Cell Type Signatures), "h" (Hallmark).
subCategory	(Optional) Sub-category; no controlled vocabulary.
ids	(Optional) Character vector of identifiers (e.g., GO, KEGG, or PMID terms).
evidenceCode	(Optional) Character vector of GO evidence codes to be included, or "ANY" (any identifier; the default). Evidence is a property of particular genes, rather than of the ontology, so evidenceCode is a convenient way of specifying how users of a GOCollection might restrict derived objects (as in done during create of a gene set from an expression set).
ontology	(Optional) Character vector of GO ontology terms to be included, or "ANY" (any identifier; the default). Unlike evidence code, ontology membership is enforced when GOCollection gene sets are constructed.
err	(Optional) logical scalar indicating whether non-existent GO terms signal an error (TRUE), or are silently ignored (FALSE).
...	Additional arguments, usually none but see specific CollectionType classes for possibilities.

Value

An object of the same class as the function name, initialized as appropriate for the collection.

Author(s)

Martin Morgan <[e-mail]>

See Also

CollectionType,

Examples

NullCollection()

## NullCollection when no collection type specified
collectionType(GeneSet())
collectionType(GeneSet(collectionType=GOCollection()))

## fl could be a url
fl <- system.file("extdata", "Broad.xml", package="GSEABase")
gs1 <- getBroadSets(fl)[[1]]
collectionType(gs1) # BroadCollection

## new BroadCollection, with different category
bc <- BroadCollection(category="c2")
## change collectionType of gs2
gs2 <- gs1
collectionType(gs2) <- NullCollection()

## OBOCollection
fl <- system.file("extdata", "goslim_plant.obo", package="GSEABase")
getOBOCollection(fl, evidenceCode="TAS") # returns OBOCollection
OBOCollection(c("GO:0008967", "GO:0015119", "GO:0030372", "GO:0002732",
                "GO:0048090"))

Example output

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: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

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

    addNode

collectionType: Null 
collectionType: Null 

collectionType: GO 
  ids:  (0 total)
  evidenceCode: EXP IDA IPI IMP IGI IEP HTP HDA HMP HGI HEP ISS ISO ISA ISM IGC IBA IBD IKR IRD RCA TAS NAS IC ND IEA 
  ontology: CC MF BP 
collectionType: Broad
  bcCategory: c1 (Positional)
  bcSubCategory: NA
collectionType: OBO 
  ids: GO:0000003, GO:0000166, ..., GO:0045182 (106 total)
  evidenceCode: TAS 
  ontology: NA 
  subsets: goslim_generic (Generic GO slim), goslim_goa (GOA and
    proteome slim), ..., gosubset_prok (Prokaryotic GO subset) (5
    total)
collectionType: OBO 
  ids: GO:0008967, GO:0015119, ..., GO:0048090 (5 total)
  evidenceCode: EXP IDA IPI IMP IGI IEP HTP HDA HMP HGI HEP ISS ISO ISA ISM IGC IBA IBD IKR IRD RCA TAS NAS IC ND IEA 
  ontology: CC MF BP 
  subsets: (0 total)

GSEABase documentation built on Dec. 13, 2020, 2 a.m.