normalize: Normalize mutational catalogues

In SigsPack: Mutational Signature Estimation for Single Samples

Description

Normalizes the catalogues to a target distribution (e.g. to match the distribution of the reference signatures).

Usage

normalize(mut_cat, source_context,
  target_context = get(utils::data("hg19context_freq", package =
  "SigsPack")))

Arguments

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)
source_context	Distribution of tri-nucleotides in the source region.
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)

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)

## Not run: 
# 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)

## End(Not run)

SigsPack documentation built on Nov. 8, 2020, 6:57 p.m.