initializeGenomeObject {AnaCoDa} | R Documentation |
initializeGenomeObject
initializes the Rcpp Genome object
initializeGenomeObject(file, genome = NULL, observed.expression.file = NULL, fasta = TRUE, simulated = FALSE, match.expression.by.id = TRUE, append = FALSE)
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) |
simulated |
boolean to determine if the data should be treated as a simulated data set (Default = FALSE). |
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). |
This function returns the initialized Genome object.
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)