A lightweight bundled assignment asset containing merged depth-2 Dominant community state type (dCST) labels for the full Valencia 13k vaginal microbiome training set.
Format
A list with five components:
- assignments
Data frame with one row per source sample and columns
sample_id(anonymized bundled-data identifier),source_row(row number in the filtered Valencia 13k source),Val_CST,Val_subCST,dcst_depth1, anddcst_depth2.- summaries
Named list of per-depth summary tables. Each table contains
depth,dcst_label,n,prop, andpath_length.- feature_labels
Character vector of source taxon labels.
- params
List recording the construction parameters.
- source
Character string documenting provenance.
Source
Generated from the VALENCIA training data at
https://github.com/ravel-lab/VALENCIA. See
data-raw/build_valencia13k_merged_dcst_depths.R and the installed
DATA_PROVENANCE.md file.
Details
The asset is computed from the Valencia 13k compositional matrix after
L-infinity normalization. dCSTs use n0 = 50 and the merged
low.freq.policy = "absorb" view, so samples from low-support
provisional states are reassigned to retained states rather than stored as
explicit rare buckets.
Examples
data(valencia13k_dcst_depth2_merged)
nrow(valencia13k_dcst_depth2_merged$assignments)
#> [1] 12881
head(valencia13k_dcst_depth2_merged$summaries$depth2)
#> depth dcst_label n prop
#> 1 2 Lactobacillus_iners__Gardnerella_vaginalis 1512 0.11738219
#> 2 2 Lactobacillus_crispatus__Lactobacillus_jensenii 972 0.07545998
#> 3 2 Lactobacillus_crispatus__Lactobacillus_iners 868 0.06738607
#> 4 2 Gardnerella_vaginalis__Atopobium_vaginae 819 0.06358202
#> 5 2 Lactobacillus_iners__Lactobacillus_jensenii 746 0.05791476
#> 6 2 Lactobacillus_crispatus__g_Lactobacillus 684 0.05310147
#> path_length
#> 1 2
#> 2 2
#> 3 2
#> 4 2
#> 5 2
#> 6 2