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

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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.

Author
Christian Arnold [aut, cre], Pooja Bhat [aut], Judith Zaugg [aut]
Date of publication
None
Maintainer
Christian Arnold <christian.arnold@embl.de>
License
LGPL (>= 3)
Version
1.4.1

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.

Files in this package

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