Last data update: 2014.03.03

SummarizedExperiment

Package: SummarizedExperiment
Title: SummarizedExperiment container
Description: The SummarizedExperiment container contains one or more assays,
each represented by a matrix-like object of numeric or other mode.
The rows typically represent genomic ranges of interest and the columns
represent samples.
Version: 1.2.3
Encoding: UTF-8
Author: Martin Morgan, Valerie Obenchain, Jim Hester, Hervé Pagès
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
biocViews: Genetics, Infrastructure, Sequencing, Annotation, Coverage,
GenomeAnnotation
Depends: R (>= 3.2), methods, GenomicRanges (>= 1.23.15), Biobase
Imports: utils, stats, BiocGenerics (>= 0.15.3), S4Vectors (>= 0.9.36),
IRanges (>= 2.5.26), GenomeInfoDb
Suggests: annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures,
TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown,
digest, jsonlite, rhdf5, airway
VignetteBuilder: knitr
License: Artistic-2.0
Collate: utils.R Assays-class.R SummarizedExperiment-class.R
RangedSummarizedExperiment-class.R intra-range-methods.R
inter-range-methods.R coverage-methods.R findOverlaps-methods.R
nearest-methods.R makeSummarizedExperimentFromExpressionSet.R
readKallisto.R zzz.R
NeedsCompilation: no
Packaged: 2016-06-10 05:19:12 UTC; biocbuild

● BiocViews: Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing
● 0 images, 10 functions, 0 datasets
● Reverse Depends: 35

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'SummarizedExperiment' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'SummarizedExperiment'
    finding HTML links ... done
    Assays-class                            html  
    finding level-2 HTML links ... done

Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/Assays-class.Rd:118: missing file link 'SimpleList'
    RangedSummarizedExperiment-class        html  
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:116: missing file link 'DataFrame'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:119: missing file link 'DataFrame'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:122: missing file link 'GRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:123: missing file link 'GRangesList'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:126: missing file link 'GRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:126: missing file link 'GRangesList'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:151: missing file link 'GRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:152: missing file link 'GRangesList'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:216: missing file link 'shift'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:217: missing file link 'isDisjoint'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:218: missing file link 'coverage'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:219: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:220: missing file link 'nearest'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:264: missing file link 'shift'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:265: missing file link 'isDisjoint'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:266: missing file link 'coverage'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:267: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:268: missing file link 'nearest'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:271: missing file link 'GRanges'
    SummarizedExperiment-class              html  
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/SummarizedExperiment-class.Rd:135: missing file link 'mcols'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/SummarizedExperiment-class.Rd:208: missing file link 'mcols'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/SummarizedExperiment-class.Rd:395: missing file link 'DataFrame'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/SummarizedExperiment-class.Rd:395: missing file link 'SimpleList'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/SummarizedExperiment-class.Rd:396: missing file link 'Annotated'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/SummarizedExperiment-class.Rd:398: missing file link 'metadata'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/SummarizedExperiment-class.Rd:399: missing file link 'mcols'
    coverage-methods                        html  
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/coverage-methods.Rd:26: missing file link 'coverage'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/coverage-methods.Rd:34: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/coverage-methods.Rd:34: missing file link 'GRangesList'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/coverage-methods.Rd:40: missing file link 'coverage'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/coverage-methods.Rd:42: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/coverage-methods.Rd:42: missing file link 'GRangesList'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/coverage-methods.Rd:47: missing file link 'coverage'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/coverage-methods.Rd:55: missing file link 'coverage'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/coverage-methods.Rd:57: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/coverage-methods.Rd:58: missing file link 'GRangesList'
    findOverlaps-methods                    html  
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/findOverlaps-methods.Rd:43: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/findOverlaps-methods.Rd:47: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/findOverlaps-methods.Rd:55: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/findOverlaps-methods.Rd:55: missing file link 'GRangesList'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/findOverlaps-methods.Rd:63: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/findOverlaps-methods.Rd:65: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/findOverlaps-methods.Rd:65: missing file link 'GRangesList'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/findOverlaps-methods.Rd:70: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/findOverlaps-methods.Rd:78: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/findOverlaps-methods.Rd:80: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/findOverlaps-methods.Rd:81: missing file link 'GRangesList'
    inter-range-methods                     html  
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/inter-range-methods.Rd:30: missing file link 'isDisjoint'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/inter-range-methods.Rd:38: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/inter-range-methods.Rd:38: missing file link 'GRangesList'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/inter-range-methods.Rd:48: missing file link 'isDisjoint'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/inter-range-methods.Rd:50: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/inter-range-methods.Rd:50: missing file link 'GRangesList'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/inter-range-methods.Rd:55: missing file link 'isDisjoint'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/inter-range-methods.Rd:63: missing file link 'isDisjoint'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/inter-range-methods.Rd:65: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/inter-range-methods.Rd:66: missing file link 'GRangesList'
    intra-range-methods                     html  
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/intra-range-methods.Rd:57: missing file link 'shift'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/intra-range-methods.Rd:61: missing file link 'shift'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/intra-range-methods.Rd:65: missing file link 'shift'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/intra-range-methods.Rd:69: missing file link 'shift'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/intra-range-methods.Rd:73: missing file link 'shift'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/intra-range-methods.Rd:81: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/intra-range-methods.Rd:81: missing file link 'GRangesList'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/intra-range-methods.Rd:91: missing file link 'shift'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/intra-range-methods.Rd:93: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/intra-range-methods.Rd:93: missing file link 'GRangesList'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/intra-range-methods.Rd:101: missing file link 'shift'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/intra-range-methods.Rd:103: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/intra-range-methods.Rd:104: missing file link 'GRangesList'
    makeSummarizedExperimentFromExpressionSet
                                            html  
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:17: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:19: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:38: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:41: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:44: missing file link 'rownames'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:44: missing file link 'GRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:46: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:63: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:69: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:78: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:80: missing file link 'TxDb'
    nearest-methods                         html  
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/nearest-methods.Rd:66: missing file link 'nearest'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/nearest-methods.Rd:79: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/nearest-methods.Rd:79: missing file link 'GRangesList'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/nearest-methods.Rd:88: missing file link 'nearest'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/nearest-methods.Rd:90: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/nearest-methods.Rd:90: missing file link 'GRangesList'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/nearest-methods.Rd:95: missing file link 'nearest'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/nearest-methods.Rd:103: missing file link 'nearest'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/nearest-methods.Rd:105: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpYrYSQa/R.INSTALL5c912c49413c/SummarizedExperiment/man/nearest-methods.Rd:106: missing file link 'GRangesList'
    readKallisto                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SummarizedExperiment)
Making 'packages.html' ... done

Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO