SNPhood

Package: SNPhood
Title: SNPhood: Investigate, quantify and visualise the epigenomic
neighbourhood of SNPs using NGS data
Version: 1.2.2
Authors@R: c(person("Christian", "Arnold", email =
"christian.arnold@embl.de", role = c("cre","aut")),
person("Pooja", "Bhat", email = "pooja.bhat@embl.de", role =
"aut"), person("Judith", "Zaugg", email =
"judith.zaugg@embl.de", role = "aut"))
Author: Christian Arnold [aut, cre], Pooja Bhat [aut], Judith Zaugg
[aut]
Maintainer: Christian Arnold <christian.arnold@embl.de>
Description: To date, thousands of single nucleotide polymorphisms (SNPs) have
been found to be associated with complex traits and diseases. However, the vast
majority of these disease-associated SNPs lie in the non-coding part of the
genome, and are likely to affect regulatory elements, such as enhancers and
promoters, rather than function of a protein. Thus, to understand the molecular
mechanisms underlying genetic traits and diseases, it becomes increasingly
important to study the effect of a SNP on nearby molecular traits such as
chromatin environment or transcription factor (TF) binding. Towards this aim, we
developed SNPhood, a user-friendly *Bioconductor* R package to investigate and
visualize the local neighborhood of a set of SNPs of interest for NGS data such
as chromatin marks or transcription factor binding sites from ChIP-Seq or RNA-
Seq experiments. SNPhood comprises a set of easy-to-use functions to extract,
normalize and summarize reads for a genomic region, perform various data quality
checks, normalize read counts using additional input files, and to cluster
and visualize the regions according to the binding pattern. The regions around
each SNP can be binned in a user-defined fashion to allow for analysis of very
broad patterns as well as a detailed investigation of specific binding shapes.
Furthermore, SNPhood supports the integration with genotype information to
investigate and visualize genotype-specific binding patterns. Finally, SNPhood
can be employed for determining, investigating, and visualizing allele-specific
binding patterns around the SNPs of interest.
Imports: DESeq2, cluster, ggplot2, lattice, GenomeInfoDb, BiocParallel,
VariantAnnotation, BiocGenerics, IRanges, methods,
SummarizedExperiment, RColorBrewer, Biostrings,
grDevices, gridExtra, stats, grid, utils, graphics, reshape2,
scales, S4Vectors
Depends: R (>= 3.2), GenomicRanges, Rsamtools, data.table, checkmate
Suggests: BiocStyle, knitr, rmarkdown, SNPhoodData, corrplot, pryr
VignetteBuilder: knitr
biocViews: Software
License: LGPL (>= 3)
LazyData: true
BugReports: christian.arnold@embl.de
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-16 05:50:19 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'SNPhood' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'SNPhood'
    finding HTML links ... done
    SNPhood-class                           html  
    SNPhood                                 html  
    SNPhood.o                               html  
    analyzeSNPhood                          html  
    finding level-2 HTML links ... done

    annotation-methods                      html  
    annotationBins                          html  
    annotationBins2                         html  
    annotationDatasets                      html  
    annotationReadGroups                    html  
    annotationRegions                       html  
    associateGenotypes                      html  
    bins-methods                            html  
    changeObjectIntegrityChecking           html  
    collectFiles                            html  
Rd warning: /tmp/Rtmp1I3QTZ/R.INSTALL6f237f2de7cc/SNPhood/man/collectFiles.Rd:46: missing file link 'path'
    convertToAllelicFractions               html  
    counts-method                           html  
    datasets-methods                        html  
    deleteDatasets                          html  
    deleteReadGroups                        html  
    deleteRegions                           html  
    enrichment-methods                      html  
    getDefaultParameterList                 html  
    mergeReadGroups                         html  
    parameters-methods                      html  
    plotAllelicBiasResults                  html  
    plotAllelicBiasResultsOverview          html  
    plotAndCalculateCorrelationDatasets     html  
    plotAndCalculateWeakAndStrongGenotype   html  
    plotAndClusterMatrix                    html  
    plotBinCounts                           html  
    plotClusterAverage                      html  
    plotGenotypesPerCluster                 html  
    plotGenotypesPerSNP                     html  
    plotRegionCounts                        html  
    readGroups-methods                      html  
    regions-methods                         html  
    renameBins                              html  
    renameDatasets                          html  
    renameReadGroups                        html  
    renameRegions                           html  
    results                                 html  
    testForAllelicBiases                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SNPhood)
Making 'packages.html' ... done