addObservedSynthesisRateSet: Add gene observed synthesis rates

In AnaCoDa: Analysis of Codon Data under Stationarity using a Bayesian Framework

Description

addObservedSynthesisRateSet returns the observed synthesis rates of the genes within the genome specified.

Usage

addObservedSynthesisRateSet(
  genome,
  observed.expression.file,
  match.expression.by.id = TRUE
)

Arguments

genome	A genome object initialized with initializeGenomeObject to add observed expression data.
observed.expression.file	A string containing the location of a file containing empirical expression rates (optional).
match.expression.by.id	If TRUE (default) observed expression values will be assigned by matching sequence identifier. If FALSE observed expression values will be assigned by order

Value

Returns the genome after adding the new gene expression values

Examples

genome_file <- system.file("extdata", "genome.fasta", package = "AnaCoDa")
expression_file <- system.file("extdata", "expression.csv", package = "AnaCoDa") 
## reading genome
genome <- initializeGenomeObject(file = genome_file)


## add expression values after the genome was initiallized, 
## or adding an additional set of expression values
genome <- addObservedSynthesisRateSet(genome = genome, 
                   observed.expression.file = expression_file)

AnaCoDa documentation built on Jan. 8, 2021, 2:37 a.m.