filterForDeaminase: Convenience function that filters a with tri-nucleotide...
In Wedge-lab/dpclust3p: Dirichlet Process Clustering Pre-Processing Package

filterForDeaminase

R Documentation

Convenience function that filters a with tri-nucleotide context annotated list of loci for cytosine deaminase signature, or C>T at CpG.

Convenience function that filters a with tri-nucleotide context annotated list of loci for cytosine deaminase signature, or C>T at CpG.

filterForDeaminase(
  loci_file,
  outfile,
  ref_genome,
  trinucleotide_column = 5,
  alt_allele_column = 4
)

`loci_file`	Filepath to a with tri-nucleotide context annotated loci
`outfile`	Filepath to where to store the output.
`ref_genome`	Full path to an indexed reference genome fasta file
`trinucleotide_column`	Integer representing the column within the input file that contains the context
`alt_allele_column`	The column in the annotated loci file that contains the reference base.