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

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

Description

Return the annotation of the SNP regions that are defined in the SNPhood object.

Usage

annotationRegions(SNPhood.o, asGRangesObj = FALSE, verbose = FALSE)

Arguments

SNPhood.o	Object of class SNPhood
asGRangesObj	Logical(1). Default FALSE. Should the full annotation be returned (as GRanges object) or only the annotation of the SNP regions (as character vector)?
verbose	Logical(1). Default FALSE. Should the verbose mode (i.e., diagnostic messages during execution of the script) be enabled?

Value

If asGRangesObj is set to TRUE, a GRanges object is returned. Otherwise, a character vector with the currently stored SNP annotation is returned.

Examples

data(SNPhood.o, package="SNPhood")
IDs.vec = annotationRegions(SNPhood.o, asGRangesObj = FALSE)
IDs.gr  = annotationRegions(SNPhood.o, asGRangesObj = TRUE)

SNPhood documentation built on Nov. 8, 2020, 6:22 p.m.