replicates_OTUs: OTU (TRF) matrices for a suite of replicate MTRFLP samples

Description Usage Format Details Source


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.

TREX settings

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.

mixtrak/wellington.aquifer.ecol documentation built on Nov. 30, 2017, 4:25 a.m.