Annotate CpG sites — annotate_cpg

A simple method to test whether your trinucleotide context contains a CpG site. Vectorized version of Biostrings::vcountPattern is used.

Usage

annotate_cpg_sites(mutation_data, motif = "CG", column_query = "context", ...)

Arguments

mutation_data: A dataframe or GRanges object containing the genomic regions of interest in which to look for CpG sites.
motif: Default "CG", which returns CpG sites. You could in theory use an arbitrary string to look at different motifs. Use with caution. In this case the pattern being searched must be a column in the mutation data.
column_query: Default "context" but can be any column in the mutation data that you wish to look for a motif in.
...: Additional arguments to vcountPattern()

Value

A data frame with the same number of rows as there were ranges in the input, but with an additional metadata column indicating CpG sites in the target sequence of the mutation.