SNPhood: SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
Version 1.6.0

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]
Bioconductor views Software
Date of publicationNone
MaintainerChristian Arnold <christian.arnold@embl.de>
LicenseLGPL (>= 3)
Version1.6.0
URL https://bioconductor.org/packages/SNPhood
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SNPhood")

Getting started

Introduction and Methodological Details
Workflow example

Popular man pages

annotationBins: Get the annotation(names) of the bins in a _SNPhood_ object.
collectFiles: Helper function to generate a data frame that can be used as...
getDefaultParameterList: Helper function to generate a default parameter list as input...
plotAndCalculateWeakAndStrongGenotype: Visualizes and calculates strong and weak genotypes.
plotAndClusterMatrix: Clustering of read counts or enrichmens across bins for a...
plotFDRResults: Graphically summarize the results of the allelic bias...
SNPhood.o: SNPhood example data
See all...

All man pages Function index File listing

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...
plotAndSummarizeAllelicBiasTest: Summarize the allelic bias analysis across SNP regions and...
plotBinCounts: Visualize counts or enrichment for a particular region across...
plotClusterAverage: Visualize average enrichment per cluster
plotFDRResults: Graphically summarize the results of the allelic bias...
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

BAMHeaderConsistencyChecks Source code
SNPhood Man page
SNPhood-class Man page
SNPhood-data Man page
SNPhood-package Man page
SNPhood.o Man page
analyzeSNPhood Man page Source code
annotation Man page
annotation,SNPhood-method Man page
annotationBins Man page Source code
annotationBins2 Man page Source code
annotationDatasets Man page Source code
annotationReadGroups Man page Source code
annotationRegions Man page Source code
associateGenotypes Man page Source code
bins Man page
calcBinLabelsPlot Source code
calcBinomTestVector Source code
calcRandomBackgroundDistr Source code
calculateGenomeWideBackground Source code
calculateOverlapsBin Source code
calculateOverlapsReads Source code
changeObjectIntegrityChecking Man page Source code
checkAndConvertDatasetArgument Source code
checkAndConvertReadGroupArgument Source code
checkAndConvertRegionArgument Source code
checkAndCreateIndexFile Source code
checkConfigFile Source code
checkObjectValidity Source code
collectFiles Man page Source code
collectFilesGen Source code
constructScanBamFlags Source code
constructScanBamFlagsGen Source code
convertToAllelicFractions Man page Source code
counts Man page
counts,SNPhood-method Man page
createBins Source code
createSNPhoodObject Source code
datasets Man page
deleteDatasets Man page Source code
deleteReadGroups Man page Source code
deleteRegions Man page Source code
dentifyGenotypeIncompatibilities Source code
desat Source code
determineHeterozygosity Source code
enrichment Man page
enrichment,SNPhood-method Man page
execInParallelGen Source code
extractAndNormalize Source code
extractFromBAM Source code
extractFromBAMGen Source code
extractGenotypesVCF Source code
filterReads Source code
generateClusterPlot Source code
generateColorsForReadGroupsAndDatasets Source code
generateDefaultReadFlags Source code
getAnnotation Source code
getBinAxisLabelsForGGPlot Source code
getBinLabelXAxis Source code
getBinLabelYAxis Source code
getCounts Source code
getDefaultParameterList Man page Source code
getEnrichment Source code
getErrorForOnlyPrepareSamplesCorrelation Source code
getErrorMessageReadGroupSpecificty Source code
getFieldsForBAMParsing Source code
getGenomeData Source code
getListOfSupportedParameters Source code
getMemoryProfile Source code
getParameters Source code
getSNPGRangesObj Source code
getThemeForGGPlot Source code
getUniqueMappabilityData Source code
getVerticalLineForGGPlot Source code
getXLab Source code
getYLab Source code
mergeReadGroups Man page Source code
nBins Man page Source code
nDatasets Man page Source code
nReadGroups Man page Source code
nRegions Man page Source code
nitBiocParallel Source code
nitSNPhoodObject Source code
normalizeMatrixForClustering Source code
onAttach Source code
pamClustering Source code
parameters Man page
parameters,SNPhood-method Man page
parseAndProcessUserRegions Source code
parseBed6File Source code
plotAllelicBiasResults Man page Source code
plotAllelicBiasResultsOverview Man page Source code
plotAndCalculateCorrelationDatasets Man page Source code
plotAndCalculateWeakAndStrongGenotype Man page Source code
plotAndClusterMatrix Man page Source code
plotAndSummarizeAllelicBiasTest Man page Source code
plotBinCounts Man page Source code
plotClusterAverage Man page Source code Source code
plotFDRResults Man page Source code
plotGenotypesPerCluster Man page Source code
plotGenotypesPerSNP Man page Source code
plotRegionCounts Man page Source code
plotRegionFeatures Source code
prettyNum Source code
printExecutionTime Source code
produceTitleForPlot Source code
readGroups Man page
regions Man page
renameBins Man page Source code
renameDatasets Man page Source code
renameReadGroups Man page Source code
renameRegions Man page Source code
results Man page Source code
scaleLibraries Source code
testForAllelicBiases Man page Source code
validSNPhoodObj Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/DataClasses.R
R/SNPhood.R
R/core.R
R/misc.R
R/visualize.R
R/zzz.R
build
build/vignette.rds
data
data/SNPhood.o.rda
data/datalist
inst
inst/doc
inst/doc/IntroductionToSNPhood.R
inst/doc/IntroductionToSNPhood.Rmd
inst/doc/IntroductionToSNPhood.html
inst/doc/workflow.R
inst/doc/workflow.Rmd
inst/doc/workflow.html
inst/extdata
man
man-roxygen
man-roxygen/SNPhood.R
man-roxygen/colorPalette.R
man-roxygen/dataset.R
man-roxygen/datasets.R
man-roxygen/fileToPlot.R
man-roxygen/ggplotReturn.R
man-roxygen/maxWidthLabels.R
man-roxygen/nClusters.R
man-roxygen/normalize.R
man-roxygen/object.R
man-roxygen/plotChr.R
man-roxygen/plotEndPos.R
man-roxygen/plotGraph.R
man-roxygen/plotRegionBoundaries.R
man-roxygen/plotRegionLabels.R
man-roxygen/plotStartPos.R
man-roxygen/printPlot.R
man-roxygen/readGroup.R
man-roxygen/readGroupColors.R
man-roxygen/readGroups.R
man-roxygen/region.R
man-roxygen/regions.R
man-roxygen/returnOnlyPlotNotObject.R
man-roxygen/signThreshold.R
man-roxygen/sizePoints.R
man-roxygen/verbose_FALSE.R
man-roxygen/verbose_TRUE.R
man-roxygen/ylim.R
man/SNPhood-class.Rd
man/SNPhood.Rd
man/SNPhood.o.Rd
man/analyzeSNPhood.Rd
man/annotation-methods.Rd
man/annotationBins.Rd
man/annotationBins2.Rd
man/annotationDatasets.Rd
man/annotationReadGroups.Rd
man/annotationRegions.Rd
man/associateGenotypes.Rd
man/bins-methods.Rd
man/changeObjectIntegrityChecking.Rd
man/collectFiles.Rd
man/convertToAllelicFractions.Rd
man/counts-method.Rd
man/datasets-methods.Rd
man/deleteDatasets.Rd
man/deleteReadGroups.Rd
man/deleteRegions.Rd
man/enrichment-methods.Rd
man/getDefaultParameterList.Rd
man/mergeReadGroups.Rd
man/parameters-methods.Rd
man/plotAllelicBiasResults.Rd
man/plotAllelicBiasResultsOverview.Rd
man/plotAndCalculateCorrelationDatasets.Rd
man/plotAndCalculateWeakAndStrongGenotype.Rd
man/plotAndClusterMatrix.Rd
man/plotAndSummarizeAllelicBiasTest.Rd
man/plotBinCounts.Rd
man/plotClusterAverage.Rd
man/plotFDRResults.Rd
man/plotGenotypesPerCluster.Rd
man/plotGenotypesPerSNP.Rd
man/plotRegionCounts.Rd
man/readGroups-methods.Rd
man/regions-methods.Rd
man/renameBins.Rd
man/renameDatasets.Rd
man/renameReadGroups.Rd
man/renameRegions.Rd
man/results.Rd
man/testForAllelicBiases.Rd
vignettes
vignettes/IntroductionToSNPhood.Rmd
vignettes/figs
vignettes/figs/Comparison.png
vignettes/figs/Input.png
vignettes/figs/Logo.png
vignettes/figs/SNPhood_workflow_detailed.png
vignettes/figs/SNPhood_workflow_simple.png
vignettes/figs/genotype.png
vignettes/figs/inputFileFlexibility.png
vignettes/figs/inputNormalizationScheme.png
vignettes/figs/normDetails.png
vignettes/figs/readFiltering.png
vignettes/workflow.Rmd
SNPhood documentation built on May 20, 2017, 9:20 p.m.

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