% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/normalize.R
 \name{normalize}
 \alias{normalize}
 \title{Normalize mutational catalogues}
 \usage{
 normalize(mut_cat, source_context,
   target_context = get(utils::data("hg19context_freq", package =
   "SigsPack")))
 }
 \arguments{
 \item{mut_cat}{mutational catalogues (96 by n, n being the amounts of 
 catalogues) that will be normalized. The tri-nucleotide contexts are expected 
 to be in the default lexicographical order (see simulated data or cosmicSigs)}
 
 \item{source_context}{Distribution of tri-nucleotides in the source region.}
 
 \item{target_context}{Distribution of tri-nucleotides in the target region.
 Defaults to the context frequencies of BSgenome.Hsapiens.UCSC.hg19 since that
 corresponds to the COSMIC signatures}
 }
 \value{
 mutational catalogues (96 by n, n being the amounts of catalogues) 
 normalized to match the target distribution (context)
 }
 \description{
 Normalizes the catalogues to a target distribution (e.g. to match the 
 distribution of the reference signatures).
 }
 \note{
 The output from get_context_freq() can be used as input to this 
 function
 }
 \examples{
 # this is a toy example:
 #create mutational catalogue:
 sim_data <- create_mut_catalogues(1, 500)[['catalogues']]
 # get trinucleotide frequencies for the genome:
 genome_context <- get_context_freq(BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19)
 #get trinucleotide frequencies for a specific region:
 gr<-GenomicRanges::GRanges(seqnames=c("chr1"),
           ranges=IRanges::IRanges(start=c(100000),end=c(1000000)),
           strand=c("+"))
 region_context<-get_context_freq(BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19, gr)
 #normalize data:
 normalized_mut_cat <- normalize(sim_data, region_context, genome_context)
 
 \dontrun{
 # get the tri-nucleotide distribution of an exome region
 exome_contexts <- get_context_freq(BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19,
                                    'example_exome.bed')
 
 # normalize the mutational catalogue to match the COSMIC signatures
 normalized_mut_cat <- normalize(mut_cat, exome_contexts, hg19context_freq)
 }
 
 }