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Low level interface function with GATAI

Source: R/GATAI.R
GATAI.Rd

This function interfaces with the GATAI software which removes the genes that create the PlotSignature pattern.

Usage

GATAI(
  ExpressionSet,
  singlecell_data = FALSE,
  gatai_results_path = tempdir(),
  result_overwrite = FALSE,
  condaenv = NULL
)

Arguments

ExpressionSet

a standard PhyloExpressionSet, DivergenceExpressionSet or PolymorphismsExpressionSet object.

singlecell_data

a logical value indicating whether or not the input ExpressionSet is a single cell dataset.

gatai_results_path

where shall GATAI results be stored. Default gatai_results_path = tempdir().

result_overwrite

Logical value indicating whether local results of previous GATAI run should be over-written and re-computed?

condaenv

The conda environment to use. For use_condaenv, this can be the name, the absolute prefix path, or the absolute path to the python binary. If the name is ambiguous, the first environment is used and a warning is issued. For use_miniconda, the only conda installation searched is the one installed by install_miniconda.

Author

Filipa Martins Costa and Hajk-Georg Drost