GATAI: Low level interface function with GATAI

In drostlab/myTAI: Evolutionary Transcriptomics

Low level interface function with GATAI

Description

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(s)

Filipa Martins Costa and Hajk-Georg Drost

drostlab/myTAI documentation built on Feb. 15, 2025, 6:44 p.m.