Object "TRF_replicates" is a list containing OTU abundance matrices (based on T-RF peak area) as output by the TREX web platform and processed in the vignette "TREX_processing".
A list containing 32 numerical matrices, each with different numbers of columns but with 27 rows.
Each matrix is named with a prefix A - H to denote the combination of TREX data processing settings used.
Each matrix contains OTU data for Archaea, Bacteria, Fungi or Eukarya, and is named with a corresponding suffix.
The analysis parameters varied are: noise filtering (1 vs. 1.5 standard deviations); T-RF bin width (0.5 vs 1 bp either side of max/min peaks); and permitting multiple peaks within a sample per T-RF (yes vs no). This generates 8x combinations of settings. Sample codes corresponding to combinations of parameter settings are given in vignette("optimal_TREX_diversity"). In addition, there are data for 4x taxa (Archaea, Bacteria, Fungi, Eukarya), within each perumutation of settings, generating a total of 32x data matrices.
Personal lab work.
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