AnaCoDa (version 0.1.0)

initializeGenomeObject: Genome Initialization

Description

initializeGenomeObject initializes the Rcpp Genome object

Usage

initializeGenomeObject(file, genome = NULL, observed.expression.file = NULL,
  fasta = TRUE, match.expression.by.id = TRUE, append = FALSE)

Arguments

file

A file of coding sequences in fasta or RFPData format

genome

A genome object can be passed in to concatenate the input file to it (optional).

observed.expression.file

A string containing the location of a file containing empirical expression rates (optional).

fasta

A boolean value which decides whether to initialize with a fasta file or an RFPData file. (TRUE for fasta, FALSE for RFPData)

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.

append

If TRUE (FALSE is default), function will read in additional genome data to append to an existing genome. If FALSE, genome data is cleared before reading in data (no preexisting data).

Value

This function returns the initialized Genome object.

Examples

# NOT RUN {
genome_file <- system.file("extdata", "genome.fasta", package = "AnaCoDa")
genes_file <- system.file("extdata", "more_genes.fasta", package = "AnaCoDa")
expression_file <- system.file("extdata", "expression.csv", package = "AnaCoDa")
 
## reading genome
genome <- initializeGenomeObject(file = genome_file)

## reading genome and observed expression data
genome <- initializeGenomeObject(file = genome_file, observed.expression.file = expression_file)
 
## add aditional genes to existing genome
genome <- initializeGenomeObject(file = genome_file)
genome <- initializeGenomeObject(file = genes_file, genome = genome, append = TRUE)   

# }