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

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

Description

annotationBins2 is a helper function that returns annotation of the bins that are defined in the SNPhood object.

Usage

annotationBins2(SNPhood.o, regions = NULL, fullAnnotation = FALSE,
  verbose = TRUE)

Arguments

SNPhood.o	Object of class SNPhood
regions	Integer or character. Default NULL. A subset of the SNP regions for which annotation is needed. Either the row numbers or the rownames(IDs) of the SNP regions are supported.
fullAnnotation	Logical(1). Should the full annotation(as a data.frame) be returned or only the annotation of the bins(as a character vector)?
verbose	Logical(1). Default TRUE. Should the verbose mode (i.e., diagnostic messages during execution of the script) be enabled?

Value

If fullAnnotation is set to TRUE, a data.frame with the full annotation of the bins for the(subset of) SNP regions is returned. Otherwise, a character vector with only the annotation of the bins is returned.

Warning

The number of returned bins can easily be very large, in the order of millions. Be careful because the memory consumption due the resulting object may increase considerably. Reduce memory requirements by returning only a subset of SNP regions

Examples

data(SNPhood.o, package="SNPhood")
annotation.df  = annotationBins2(SNPhood.o, regions = 1:10, fullAnnotation = TRUE)
annotation.vec = annotationBins2(SNPhood.o, regions = 1:10, fullAnnotation = FALSE)

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