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Correlation Analysis

🚧 Experimental

This command is implemented and usable, but still under active development.

The correlate command will analyze the distribution and abundance patterns of viral sequences across multiple samples to identify potential relationships (i.e. potential genome fragments / segments) and improve/guide genome binning.

Usage

rolypoly correlate -i abundance_table.tsv -o correlate

Common options

  • -i, --input: Contig x sample table (presence/absence or abundance)
  • -o, --output-prefix: Output prefix
  • -m, --mode: correlation, cooccurrence, or both
  • --method: Correlation method (spearman, pearson)
  • --table-type: auto, presence-absence, or abundance
  • --min-correlation: Threshold for reporting pairs