Creates a GO feature MSnSet

Description

Creates a new "MSnSet" instance populated with a GO term binary matrix based on an original object.

Usage

makeGoSet(object, params, namespace = "cellular_component", evidence = NULL)

Arguments

Value

A new "MSnSet" with the GO terms for the respective features in the original object.

Author(s)

Laurent Gatto

Examples

library("pRolocdata")
data(dunkley2006)
data(dunkley2006params)
goset <- makeGoSet(dunkley2006[1:10, ],
                   dunkley2006params)
goset
exprs(goset)[1:10, 1:5]
image(goset)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(pRoloc)
Loading required package: MSnbase
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: 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: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 1.20.7 
  Read '?MSnbase' and references therein for information
  about the package and how to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws

Loading required package: MLInterfaces
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 objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML
Loading required package: cluster

This is pRoloc version 1.12.4 
  Read '?pRoloc' and references therein for information
  about the package and how to get started.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/pRoloc/makeGoSet.Rd_%03d_medium.png", width=480, height=480)
> ### Name: makeGoSet
> ### Title: Creates a GO feature 'MSnSet'
> ### Aliases: makeGoSet
> 
> ### ** Examples
> 
> library("pRolocdata")

This is pRolocdata version 1.10.0.
Use 'pRolocdata()' to list available data sets.
> data(dunkley2006)
> data(dunkley2006params)
> goset <- makeGoSet(dunkley2006[1:10, ],
+                    dunkley2006params)
> goset
MSnSet (storageMode: lockedEnvironment)
assayData: 10 features, 21 samples 
  element names: exprs 
protocolData: none
phenoData: none
featureData
  featureNames: AT1G09210 AT1G21750 ... AT1G07810 (10 total)
  fvarLabels: assigned evidence ... markers (8 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
- - - Processing information - - -
Constructed GO set using cellular_component namespace: Thu Jul  7 01:44:18 2016 
 MSnbase version: 1.20.7 
> exprs(goset)[1:10, 1:5]
          GO:0005739 GO:0005773 GO:0005783 GO:0005788 GO:0048046
AT1G09210          1          1          1          1          1
AT1G21750          0          1          1          1          0
AT1G51760          0          0          1          1          0
AT1G56340          1          0          1          1          1
AT2G32920          0          1          1          1          0
AT2G47470          0          0          1          0          0
AT3G54960          0          0          1          1          0
AT4G24190          1          1          1          1          1
AT5G60640          1          0          1          1          0
AT1G07810          0          0          1          0          0
> image(goset)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>