SNPhood: SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data

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.

AuthorChristian Arnold [aut, cre], Pooja Bhat [aut], Judith Zaugg [aut]
Date of publicationNone
MaintainerChristian Arnold <christian.arnold@embl.de>
LicenseLGPL (>= 3)
Version1.4.1

View on Bioconductor

Man pages

analyzeSNPhood: Main function of _SNPhood_

annotationBins: Get the annotation(names) of the bins in a _SNPhood_ object.

annotationBins2: Get the annotation(names) of bins in a _SNPhood_ object.

annotationDatasets: Get the annotation(names) of the datasets in a _SNPhood_...

annotation-methods: Retrieve the annotation of a 'SNPhood' object.

annotationReadGroups: Get the annotation(names) of the read groups in a _SNPhood_...

annotationRegions: Get the annotation of SNP regions for a _SNPhood_ object.

associateGenotypes: Associate genotypes with user regions from a _SNPhood_...

bins-methods: Get the number of bins for a _SNPhood_ object.

changeObjectIntegrityChecking: Disable object integrity checking for a _SNPhood_ object.

collectFiles: Helper function to generate a data frame that can be used as...

convertToAllelicFractions: Convert read counts across read groups to relative fractions...

counts-method: Extract count data from a 'SNPhood' object.

datasets-methods: Get the number of datasets for a _SNPhood_ object.

deleteDatasets: Delete a particular set of datasets from a _SNPhood_ object.

deleteReadGroups: Delete a particular set of read groups.

deleteRegions: Delete a set of user regions from a _SNPhood_ object.

enrichment-methods: Extract enrichment data from an object.

getDefaultParameterList: Helper function to generate a default parameter list as input...

mergeReadGroups: Merges the counts of all read groups for a _SNPhood_ object

parameters-methods: Retrieve the parameters of an object.

plotAllelicBiasResults: Graphically summarize the results of the allelic bias...

plotAllelicBiasResultsOverview: Visualize the results of the allelic bias analysis across...

plotAndCalculateCorrelationDatasets: Calculate and plot correlation of region read counts among...

plotAndCalculateWeakAndStrongGenotype: Visualizes and calculates strong and weak genotypes.

plotAndClusterMatrix: Clustering of read counts or enrichmens across bins for a...

plotBinCounts: Visualize counts or enrichment for a particular region across...

plotClusterAverage: Visualize average enrichment per cluster

plotGenotypesPerCluster: Visualize average counts/enrichment based on strong and weak...

plotGenotypesPerSNP: Plot genotype frequencies of regions across datasets.

plotRegionCounts: Visualize the raw read counts across regions or a...

readGroups-methods: Get the number of read groups for a _SNPhood_ object.

regions-methods: Get the number of SNP regions for a _SNPhood_ object.

renameBins: Rename bins.

renameDatasets: Rename datasets.

renameReadGroups: Rename read groups.

renameRegions: Rename regions.

results: Get results of various analyses performed with a 'SNPhood'...

SNPhood: SNPhood: Investigate, quantify and visualise the epigenomic...

SNPhood-class: A class to represent, investigate, quantify and visualise the...

SNPhood.o: SNPhood example data

testForAllelicBiases: Perform an allelic bias tests for each user region and bin.

Functions

analyzeSNPhood Man page
annotation Man page
annotationBins Man page
annotationBins2 Man page
annotationDatasets Man page
annotationReadGroups Man page
annotationRegions Man page
annotation,SNPhood-method Man page
associateGenotypes Man page
bins Man page
changeObjectIntegrityChecking Man page
collectFiles Man page
convertToAllelicFractions Man page
counts Man page
counts,SNPhood-method Man page
datasets Man page
deleteDatasets Man page
deleteReadGroups Man page
deleteRegions Man page
enrichment Man page
enrichment,SNPhood-method Man page
getDefaultParameterList Man page
mergeReadGroups Man page
nBins Man page
nDatasets Man page
nReadGroups Man page
nRegions Man page
parameters Man page
parameters,SNPhood-method Man page
plotAllelicBiasResults Man page
plotAllelicBiasResultsOverview Man page
plotAndCalculateCorrelationDatasets Man page
plotAndCalculateWeakAndStrongGenotype Man page
plotAndClusterMatrix Man page
plotBinCounts Man page
plotClusterAverage Man page
plotGenotypesPerCluster Man page
plotGenotypesPerSNP Man page
plotRegionCounts Man page
readGroups Man page
regions Man page
renameBins Man page
renameDatasets Man page
renameReadGroups Man page
renameRegions Man page
results Man page
SNPhood Man page
SNPhood-class Man page
SNPhood-data Man page
SNPhood.o Man page
SNPhood-package Man page
testForAllelicBiases Man page

Files

SNPhood/DESCRIPTION
SNPhood/NAMESPACE
SNPhood/NEWS
SNPhood/R
SNPhood/R/DataClasses.R SNPhood/R/SNPhood.R SNPhood/R/core.R SNPhood/R/misc.R SNPhood/R/visualize.R SNPhood/R/zzz.R
SNPhood/build
SNPhood/build/vignette.rds
SNPhood/data
SNPhood/data/SNPhood.o.rda
SNPhood/data/datalist
SNPhood/inst
SNPhood/inst/doc
SNPhood/inst/doc/IntroductionToSNPhood.R
SNPhood/inst/doc/IntroductionToSNPhood.Rmd
SNPhood/inst/doc/IntroductionToSNPhood.html
SNPhood/inst/doc/workflow.R
SNPhood/inst/doc/workflow.Rmd
SNPhood/inst/doc/workflow.html
SNPhood/inst/extdata
SNPhood/man
SNPhood/man-roxygen
SNPhood/man-roxygen/SNPhood.R
SNPhood/man-roxygen/colorPalette.R
SNPhood/man-roxygen/dataset.R
SNPhood/man-roxygen/datasets.R
SNPhood/man-roxygen/fileToPlot.R
SNPhood/man-roxygen/ggplotReturn.R
SNPhood/man-roxygen/maxWidthLabels.R
SNPhood/man-roxygen/nClusters.R
SNPhood/man-roxygen/normalize.R
SNPhood/man-roxygen/object.R
SNPhood/man-roxygen/plotChr.R
SNPhood/man-roxygen/plotEndPos.R
SNPhood/man-roxygen/plotGraph.R
SNPhood/man-roxygen/plotRegionBoundaries.R
SNPhood/man-roxygen/plotRegionLabels.R
SNPhood/man-roxygen/plotStartPos.R
SNPhood/man-roxygen/readGroup.R
SNPhood/man-roxygen/readGroupColors.R
SNPhood/man-roxygen/readGroups.R
SNPhood/man-roxygen/region.R
SNPhood/man-roxygen/regions.R
SNPhood/man-roxygen/signThreshold.R
SNPhood/man-roxygen/sizePoints.R
SNPhood/man-roxygen/verbose_FALSE.R
SNPhood/man-roxygen/verbose_TRUE.R
SNPhood/man-roxygen/ylim.R
SNPhood/man/SNPhood-class.Rd SNPhood/man/SNPhood.Rd SNPhood/man/SNPhood.o.Rd SNPhood/man/analyzeSNPhood.Rd SNPhood/man/annotation-methods.Rd SNPhood/man/annotationBins.Rd SNPhood/man/annotationBins2.Rd SNPhood/man/annotationDatasets.Rd SNPhood/man/annotationReadGroups.Rd SNPhood/man/annotationRegions.Rd SNPhood/man/associateGenotypes.Rd SNPhood/man/bins-methods.Rd SNPhood/man/changeObjectIntegrityChecking.Rd SNPhood/man/collectFiles.Rd SNPhood/man/convertToAllelicFractions.Rd SNPhood/man/counts-method.Rd SNPhood/man/datasets-methods.Rd SNPhood/man/deleteDatasets.Rd SNPhood/man/deleteReadGroups.Rd SNPhood/man/deleteRegions.Rd SNPhood/man/enrichment-methods.Rd SNPhood/man/getDefaultParameterList.Rd SNPhood/man/mergeReadGroups.Rd SNPhood/man/parameters-methods.Rd SNPhood/man/plotAllelicBiasResults.Rd SNPhood/man/plotAllelicBiasResultsOverview.Rd SNPhood/man/plotAndCalculateCorrelationDatasets.Rd SNPhood/man/plotAndCalculateWeakAndStrongGenotype.Rd SNPhood/man/plotAndClusterMatrix.Rd SNPhood/man/plotBinCounts.Rd SNPhood/man/plotClusterAverage.Rd SNPhood/man/plotGenotypesPerCluster.Rd SNPhood/man/plotGenotypesPerSNP.Rd SNPhood/man/plotRegionCounts.Rd SNPhood/man/readGroups-methods.Rd SNPhood/man/regions-methods.Rd SNPhood/man/renameBins.Rd SNPhood/man/renameDatasets.Rd SNPhood/man/renameReadGroups.Rd SNPhood/man/renameRegions.Rd SNPhood/man/results.Rd SNPhood/man/testForAllelicBiases.Rd
SNPhood/vignettes
SNPhood/vignettes/IntroductionToSNPhood.Rmd
SNPhood/vignettes/figs
SNPhood/vignettes/figs/Comparison.png
SNPhood/vignettes/figs/Input.png
SNPhood/vignettes/figs/Logo.png
SNPhood/vignettes/figs/SNPhood_workflow_detailed.png
SNPhood/vignettes/figs/SNPhood_workflow_simple.png
SNPhood/vignettes/figs/genotype.png
SNPhood/vignettes/figs/inputFileFlexibility.png
SNPhood/vignettes/figs/inputNormalizationScheme.png
SNPhood/vignettes/figs/normDetails.png
SNPhood/vignettes/figs/readFiltering.png
SNPhood/vignettes/workflow.Rmd

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