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STB-STC — Super-Taxon Approach for Human Microbes Association Studies

STB-STC is a statistical method that can identify joint effects of microbes in human disease considering the sparsity issue and utilizing the hierarchical information of taxonomy annotation. STB and STC yield better detection performance in situations where microbes are highly correlated compared to state-of-the-art differential abundance analysis approaches. We distribute one core R function (SVB-SVC.R) related to STB and STC. It performs the method (STB or STC) on a group of microbes. The script utilizes.R includes all necessary codes to support the running of SVB-SVC.R

Input Data Preparation

Extract the .SVB-SVC.R requires the microbe data to be partitioned into blocks based on hierarchical information (Genes, Family, Order, Class) beforehand and save each block as a file.

Instruction: please see data/family_STB_blk1.RData, for example, to see the format of partitioned microbe data based on the family information.

Execute the code

Run.R takes inputs of the block index (-STB or STC) to generate results.

Output file

The output results are saved in a list in the format .rda file. Please refer to results/.rda to see more details on the output file format.

  • super.var.form: gives the cut-off results
  • super.var.dis: gives the marginal association results, including effect sizes, p-values
  • otus: gives the selected microbes
  • X: the formed Super-taxon across individuals
  • Z: depth importance scores of microbes used for ranking
  • geno.transed: candidate cut-offs used for selecting best cut-off