valencia2k: Valencia 2k vaginal microbiome dataset

In linf: L-Infinity Normalization and Dominant Community State Types

Valencia 2k vaginal microbiome dataset

Description

A stratified subsample of 2,000 vaginal samples from the Valencia 13k CST-classifier training set (France et al. 2020), bundled as an example dataset for demonstrating dCST construction after L-infinity normalization.

Usage

valencia2k

Format

A list with five components:

rel

Numeric matrix (2000 x 178). Compositional relative abundances; each row sums to 1. Rows are samples, columns are taxonomic features.

cst

Data frame (2000 x 3) with columns: sample_id (character), Val_CST (Valencia CST assignment: I, II, III, IV-A, IV-B, IV-C, V), Val_subCST (Valencia sub-CST assignment: I-A, I-B, II, III-A, III-B, IV-A, IV-B, IV-C0, IV-C1, IV-C2, IV-C3, IV-C4, V).

reads

Integer vector of length 2000. Per-sample read counts after taxonomic filtering. Use sweep(valencia2k$rel, 1, valencia2k$reads, "*") to reconstruct a count-like matrix.

taxa

Character vector of 178 taxon names (column names of rel).

source

Character string documenting provenance.

Details

The subsample preserves proportional representation of all 13 Valencia sub-CSTs and was drawn with set.seed(42).

The Valencia CST classifier (France et al. 2020) assigns vaginal microbiome samples to community state types (CSTs) based on nearest-centroid classification in relative-abundance space. The original training set contains 12,881 samples and 178 taxonomic features after filtering.

This 2,000-sample subsample is intended for vignette demonstrations. The compositional matrix can be used directly with normalize.linf and downstream dCST functions. For workflows that require count-like input, reconstruct approximate counts using the reads vector.

Source

Subsampled from the VALENCIA training data at https://github.com/ravel-lab/VALENCIA. See data-raw/build_valencia2k.R and the installed DATA_PROVENANCE.md file for construction and licensing details.

References

France, M. T., Ma, B., Gajer, P., Brown, S., Humphrys, M. S., Holm, J. B., Waetjen, L. E., Brotman, R. M., & Ravel, J. (2020). VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition. Microbiome, 8(1), 166. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1186/s40168-020-00934-6")}

Examples

data(valencia2k)
dim(valencia2k$rel)           # 2000 x 178
table(valencia2k$cst$Val_CST) # CST distribution
head(valencia2k$taxa, 10)     # first 10 taxon names

linf documentation built on Aug. 5, 2026, 9:08 a.m.