annotationRegions

SNPhood.o

Logical(1). Default FALSE. Should the full annotation be returned (as <code>GRanges</code> object) or only the annotation of the SNP regions (as character vector)?

asGRangesObj

Logical(1). Default FALSE. Should the verbose mode (i.e., diagnostic messages during execution of the script) be enabled?

verbose


Return the annotation of the SNP regions that are defined in the <code>SNPhood</code> object.


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.

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

Description

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Examples