GenoSet extends RangedSummarizedExperiment by adding some
additional methods to the API. Examples include subsetting rows with a
GenomicRanges and combining this with access to assays like genoset[i,j,assay].
Extends
Class RangedSummarizedExperiment, directly.
Methods
[
signature(x = "GenoSet", i = "ANY", j = "ANY", drop = "ANY"): ...
[
signature(x = "GenoSet", i = "character", j = "ANY", drop = "ANY"): ...
[<-
signature(x = "GenoSet", i = "ANY", j = "ANY", value = "ANY"): ...
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(genoset)
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
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")'.
*** Genoset API Changes ***
The genoset class has transitioned to the
RangedSummarizedExperiment API from the eSet API (e.g. use colnames instead of sampleNames). ***
Attaching package: 'genoset'
The following object is masked from 'package:GenomicRanges':
pos
The following objects are masked from 'package:S4Vectors':
colMeans, colSums, rowMeans, rowSums
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
Warning messages:
1: multiple methods tables found for 'colMeans'
2: multiple methods tables found for 'colSums'
3: multiple methods tables found for 'rowMeans'
4: multiple methods tables found for 'rowSums'
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/genoset/GenoSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GenoSet-class
> ### Title: Class '"GenoSet"'
> ### Aliases: GenoSet-class GenoSetOrGenomicRanges-class
> ### Keywords: classes
>
> ### ** Examples
>
> showClass("GenoSet")
Class "GenoSet" [package "genoset"]
Slots:
Name: rowRanges colData
Class: GenomicRangesORGRangesList DataFrame
Name: assays NAMES
Class: Assays characterORNULL
Name: elementMetadata metadata
Class: DataFrame list
Extends:
Class "RangedSummarizedExperiment", directly
Class "GenoSetOrGenomicRanges", directly
Class "SummarizedExperiment", by class "RangedSummarizedExperiment", distance 2
Class "Vector", by class "RangedSummarizedExperiment", distance 3
Class "Annotated", by class "RangedSummarizedExperiment", distance 4
> test.sample.names = LETTERS[11:13]
> probe.names = letters[1:10]
> assays=list(matrix(31:60,nrow=10,ncol=3,dimnames=list(probe.names,test.sample.names)))
> rowRanges=GRanges(ranges=IRanges(start=1:10,width=1,names=probe.names),seqnames=c(rep("chr1",4),rep("chr3",2),rep("chrX",4)))
> colData=data.frame(matrix(LETTERS[1:15],nrow=3,ncol=5,dimnames=list(test.sample.names,letters[1:5])))
> rse=SummarizedExperiment(rowRanges=rowRanges,assays=assays,colData=colData,metadata=metadata)
> gs = GenoSet(rowRanges, assays, colData)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.