match_to_catalog: Calculates the compatibility of a list of genomes to an input...

Description Usage Arguments Value

View source: R/match_to_catalog.R

Description

Calculates the compatibility of a list of genomes to an input catalog based on likelihood and cosine similarity

Usage

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match_to_catalog(genomes, signatures, data, cluster_fractions = NULL,
  method = "median_catalog")

Arguments

genomes

a data table or matrix with snv spectra in the first ntype columns and genomes in each row

signatures

the input catalog, a data table with signature spectra in each column

data

sets the type of sequencing platform used, options are 'msk', 'seqcap', 'wgs'

method

can be 'median_catalog', 'weighted_catalog' 'cosine_simil' or 'decompose. 'median_atalog' uses the signature catalog formed by clustering genome SNV spectra and using it as a probability distribution. The 'median_catalog' method can be used with any custom signatures data frame if the user intends to provide their own signature table.

Value

A data frame that contains the input genomes and in addition columns associated to each signature in in the catalog with likelihood and cosine simil values


parklab/SigMA documentation built on Oct. 3, 2020, 9:04 a.m.