The gCMAP package provides a toolkit for comparing differential gene expression profiles through gene set enrichment analysis. Starting from normalized microarray or RNA-seq gene expression values (stored in lists of ExpressionSet and CountDataSet objects) the package performs differential expression analysis using the limma or DESeq packages. Supplying a simple list of gene identifiers, global differential expression profiles or data from complete experiments as input, users can use a unified set of several well-known gene set enrichment analysis methods to retrieve experiments with similar changes in gene expression. To take into account the directionality of gene expression changes, gCMAPQuery introduces the SignedGeneSet class, directly extending GeneSet from the GSEABase package. To increase performance of large queries, multiple gene sets are stored as sparse incidence matrices within CMAPCollection eSets. gCMAP offers implementations of 1. Fisher's exact test (Fisher, J R Stat Soc, 1922) 2. The "connectivity map" method (Lamb et al, Science, 2006) 3. Parametric and non-parametric t-statistic summaries (Jiang & Gentleman, Bioinformatics, 2007) and 4. Wilcoxon / Mann-Whitney rank sum statistics (Wilcoxon, Biometrics Bulletin, 1945) as well as wrappers for the 5. camera (Wu & Smyth, Nucleic Acid Res, 2012) 6. mroast and romer (Wu et al, Bioinformatics, 2010) functions from the limma package and 7. wraps the gsea method from the mgsa package (Bauer et al, NAR, 2010). All methods return CMAPResult objects, an S4 class inheriting from AnnotatedDataFrame, containing enrichment statistics as well as annotation data and providing simple high-level summary plots.

Package: | gCMAP |

Type: | Package |

Version: | 1.3.5 |

Date: | 2013-03-11 |

Depends: | GSEABase, limma (>= 3.15.14) |

Imports: | Biobase, BiocGenerics, methods, GSEAlm, Category, bigmemory, bigmemoryExtras (>= 1.1.2), Matrix (>= 1.0.9), parallel, annotate, genefilter, AnnotationDbi |

Suggests: | DESeq, KEGG.db, reactome.db, RUnit, GO.db, mgsa |

License: | Artistic-2.0 |

LazyLoad: | yes |

OS_type: | unix |

ByteCompile: | TRUE |

biocViews: | Bioinformatics, Microarray, Software, Pathways, Annotation |

Collate: | 'AllClasses.R' 'AllGenerics.R' 'SignedGeneSet-accessors.R' 'utility-functions.R' 'camera_score-methods.R' 'connectivity_score-methods.R' 'featureScore-methods.R' 'fisher_score-methods.R' 'geneIndex-methods.R' 'gsealm_jg_score-methods.R' 'gsealm_score-methods.R' 'incidence-methods.R' 'mgsa_score-methods.R' 'mapIdentifiers-methods.R' 'minSetSize-methods.R' 'mroast_score-methods.R' 'romer_score-methods.R' 'wilcox_score-methods.R' 'CMAPCollection-accessors.R' 'CMAPResults-accessors.R' |

Built: | R 3.0.0; ; 2013-03-11 17:13:45 UTC; unix |

Index:

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 | ```
.DESeq_nbinom Function to perform a DESeq analysis to detect
differential expression between perturbation
and control groups.
CMAPCollection-class Class '"CMAPCollection"'
CMAPResults-class Class '"CMAPResults"'
GeneSet Methods for 'GeneSet' and 'GeneColorSet'
KEGG2cmap Functions to generate species-specific
CMAPCollections from Bioconductor KEGG.db,
reactome.db or GO.db annotation packages or the
wikipathways <URL:
http://www.wikipathways.org/index.php/Download_Pathways>
project.
SignedGeneSet Construtor for SignedGeneSet
SignedGeneSet-class Class '"SignedGeneSet"'
annotate_eset_list Function to complile a data frame with
per-instance annotation for a list of eSet
objects generated by the 'splitPerturbations'
function. The output can be used directly as
sample.annotation for the 'NChannelSet'
function.
camera_score-methods Methods for Function 'camera_score' in Package
'gCMAP'
center_eSet A function to to center columns of eSet
channels on either their kernel density peak,
their mean or their median.
connectivity_score Broad CMAP gene set enrichment metrics
eSetOnDisk A function to store the assayData of an eSet
object as BigMatrix files on disk.
eset_instances A function to subset an eSet with expression
data into smaller datasets, each corresponding
to a single perturbation experiment.
featureScores-methods Methods to obtain scores for CMAPCollection
gene sets from a matrix or eSet
fisher_score-methods Hypergeometric probability of gene set
enrichment
gCMAP-package Tools for Connectivity Map-like analyses
gCMAPData Example 'NChannelSet'
geneIndex-methods Methods for Function 'geneIndex' in Package
'gCMAP'
generate_gCMAP_NChannelSet
Generate a perturbation profile library from
expression sets of control/treatment pairs
gsealm_jg_score-methods
Parametric test for testing normally
distributed scores for gene set enrichment
gsealm_score-methods Methods for Function 'gsealm_score' in Package
'gCMAP'
induceCMAPCollection-methods
Methods for Function 'induceCMAPCollection' in
Package 'gCMAP'
mapNmerge A function to map eSet featureNames and
calculate summaries for many-to-one mapping
features
matrix_or_big.matrix-class
Class '"matrix_or_big.matrix"'
memorize Create a new NChannelSet instance by selecting
specific channels and load BigMatrix assayData
into memory, if present
mergeCMAPs This function merged two eSets.
mgsa_score-methods Model-based gene set analysis (MGSA)
minSetSize GeneSetCollection length filtering
mroast_score-methods Methods for Function 'mroast_score' in Package
'gCMAP'
pairwise_DESeq Generate statistics associated with pairwise
differential expression from RNAseq count data
pairwise_compare Generate statistics associated with pairwise
differential expression
romer_score-methods Methods for Function 'romer_score' in Package
'gCMAP'
signedRankSumTest An implementation of the Wilcox rank sum test /
Mann-Whitney test that takes into account the
direction / sign of gene set members and
possibly the correlation between cases
splitPerturbations Function to split an ExpressionSet downloaded
from ArrayExpress based on the experimental
factors present in the phenoData slot
wilcox_score-methods Methods for Function 'wilcox_score' in Package
'gCMAP'
zScores Function to calculate z-scores from p-values
``` |

Further information is available in the following vignettes:

`diffExprAnalysis` | main (source) |

`gCMAP` | main (source) |

Thomas Sandmann <[email protected]>, Richard Bourgon <[email protected]> and Sarah Kummerfeld <[email protected]>

Maintainer: Thomas Sandmann <[email protected]>

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