Create a GeneDiscoveR object

This function creates a GeneDiscoveR object with the specified parameters. The data can be originated from OrthoFinder or InParanoiDB. Can be indicate the origin of the orthologs definition with the parameter orthologsTool.

GeneDiscoveR(
  overallsDir = NULL,
  N0sDir = NULL,
  dataFile = NULL,
  annotationFile = NULL,
  uniqueInflation = NULL,
  minInflation = NULL,
  maxInflation = NULL,
  stepInflation = NULL,
  pairSpeciesDir = NULL,
  principalSpecie = NULL,
  principalSpeciePrefix = NULL,
  orthologsTool = "OrthoFinder"
)

Arguments

overallsDir

The directory path for the overalls (only for OrthoFinder run).

N0sDir

The directory path for the N0s (only for OrthoFinder run).

dataFile

The file path for the table with at least two columns (speciesID and n columns one per trait or phenotype) data.

annotationFile

The file path for the annotation data.

uniqueInflation

The unique inflation value to be used (only for OrthoFinder run).

minInflation

The minimum inflation value for the range of inflations (only for OrthoFinder run).

maxInflation

The maximum inflation value for the range of inflations (only for OrthoFinder run).

stepInflation

The step size for the range of inflations (only for OrthoFinder run).

pairSpeciesDir

The directory path for the pair species (only for InParanoiDB run).

principalSpecie

The principal species (only for InParanoiDB run).

principalSpeciePrefix

The principal species prefix (only for InParanoiDB run).

orthologsTool

The tool used for orthologs identification, default is OrthoFinder (OrthoFinder or InParanoiDB).

Value

A GeneDiscoveR object with the specified parameters.

Details

For OrthoFinder, the parameters overallsDir, N0sDir, dataFile, uniqueInflation, minInflation, maxInflation, and stepInflation are required. The parameters of Inflation depend on the type of analysis to be performed with unique inflation or a range of inflations.

For InParanoiDB, the parameters pairSpeciesDir, principalSpecie, and principalSpeciePrefix are required. The comparison is made between the principal species and the other species. The principal species is the species that will be used as a reference. The principal species name is principalSpecie and the principal species gene prefix is principalSpeciePrefix.

Examples

# Create a GeneDiscoveR for an execution with multiple inflation values

N0sDir <- system.file("extdata", "N0-1dot3-6", package = "GeneDiscoveR")
overallsDir <- system.file("extdata", "Comparatives-1dot3-6", package = "GeneDiscoveR")
dataFile <- system.file("extdata", "annotatedCDSs.tsv", package = "GeneDiscoveR")
minInflation <- 1.3
maxInflation <- 6
stepInflation <- 0.1

GeneDiscoveRobject <- GeneDiscoveR(overallsDir = overallsDir, N0sDir = N0sDir, dataFile = dataFile, minInflation = minInflation, maxInflation = maxInflation, stepInflation = stepInflation)

# Create a GeneDiscoveR for an execution with only one inflation value

uniqueInflation <- 1.8

GeneDiscoveRobject <- GeneDiscoveR(N0sDir = N0sDir, dataFile = dataFile, uniqueInflation = uniqueInflation)
#> -----------From OrthoFinder-----------
#> The process has been completed successfully

# If you want to indicate the annotation file, you can use the following code:

annotationFile <- system.file("extdata", "annotatedCDSs.tsv")

GeneDiscoveRobject <- GeneDiscoveR(overallsDir = overallsDir, N0sDir = N0sDir, annotationFile = annotationFile, dataFile = dataFile, minInflation = minInflation, maxInflation = maxInflation, stepInflation = stepInflation)