deleteRegions: Delete a set of user regions from a _SNPhood_ object.

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

Description

deleteRegions deletes a set of user regions. Removal is irreversible. It is therefore recommended to save the resulting SNPhood object with a new name.

Usage

deleteRegions(SNPhood.o, regions, verbose = TRUE)

Arguments

SNPhood.o	Object of class SNPhood
regions	Numeric or Character or NULL. Default NULL. Regions that should be plotted, either specified as integer (such as 1, value must be between 1 and the total number of regions as defined in the object) or their annotation (name must appear in the region names as obtained via the function annotationRegions). If set to NULL, all regions will be considered.
verbose	Logical(1). Default TRUE. Should the verbose mode (i.e., diagnostic messages during execution of the script) be enabled?

Value

an object of class SNPhood with the requested regions being deleted.

Warning

Execution of this function resets the slot additionalResults and all of its results (e.g, allelic bias analysis). The reason for this is that all results stored in this slot are affected by the deletion of regions

See Also

deleteDatasets, deleteReadGroups

Examples

data(SNPhood.o, package="SNPhood")
# Delete the first 10 regions
SNPhood_mod.o = deleteRegions(SNPhood.o, c(1:10))

# Delete regions by their annotation
SNPhood_mod.o = deleteRegions(SNPhood.o, c("rs2822405", "rs467140"))

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