A lightweight bundled assignment asset containing merged depth-3 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,dcst_depth2, anddcst_depth3.- 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 depth-3 asset extends valencia13k_dcst_depth2_merged by one
additional hierarchical dCST refinement. All levels use n0 = 50 and
low.freq.policy = "absorb". This object is intended as a reusable
source for selecting richer VALENCIA-derived component sets without
recomputing the full hierarchy from the 13k source matrix.
Examples
data(valencia13k_dcst_depth3_merged)
nrow(valencia13k_dcst_depth3_merged$assignments)
#> [1] 12881
head(valencia13k_dcst_depth3_merged$summaries$depth3)
#> depth dcst_label
#> 1 3 Lactobacillus_crispatus__Lactobacillus_iners__Lactobacillus_jensenii
#> 2 3 Gardnerella_vaginalis__Lactobacillus_iners__Atopobium_vaginae
#> 3 3 Lactobacillus_crispatus__Lactobacillus_jensenii__g_Lactobacillus
#> 4 3 Lactobacillus_iners__Lactobacillus_crispatus__Lactobacillus_jensenii
#> 5 3 Atopobium_vaginae__Gardnerella_vaginalis__g_Fastidiosipila
#> 6 3 Gardnerella_vaginalis__Atopobium_vaginae__g_Fastidiosipila
#> n prop path_length
#> 1 442 0.03431411 3
#> 2 416 0.03229563 3
#> 3 372 0.02887975 3
#> 4 323 0.02507569 3
#> 5 308 0.02391119 3
#> 6 295 0.02290195 3