initializeGenomeObject {AnaCoDa}

Genome Initialization

Description

initializeGenomeObject initializes the Rcpp Genome object

Usage

initializeGenomeObject(
  file,
  genome = NULL,
  observed.expression.file = NULL,
  fasta = TRUE,
  positional = FALSE,
  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

String containing the location of a file containing empirical expression rates (optional). Default value is NULL.

fasta

Boolean value indicating whether file argument is a fasta file (TRUE) or an RFPData file (FALSE). Default value is TRUE.

positional

Boolean indicating if the positional information in the RFPData file is necessary. Default value is FALSE

match.expression.by.id

If TRUE, observed expression values will be assigned by matching sequence identifier. If FALSE, observed expression values will be assigned by order. Default value is TRUE.

append

If TRUE, 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). Default value is FALSE.

Value

This function returns the initialized Genome object.

Examples

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)