HMP Illumina 16S Giant-Component Graph

A symmetric k-nearest-neighbor graph constructed from samples from the Ravel-led University of Maryland Baltimore Human Microbiome Project (UMB-HMP) longitudinal vaginal cohort, generated by Illumina 16S rRNA amplicon sequencing. Rows without an explicit HMP project label, rows from the related U01 cohort, and legacy 454 runs are excluded before preprocessing.

Usage

hmp.gc

Format

A named list with components:

adj_list

Adjacency list with 1-based integer neighbor indices.

weight_list

Parallel list of Euclidean edge lengths in the ten-component PCA representation.

vertex_data

Data frame with one row per HMP sample and columns for sample identifier, HMP project, sequencing platform and phase, CST and subCST annotations, and retained-read diagnostics.

graph_info

Named list recording the cohort filter, representation, graph constructor, selected k, and graph dimensions.

Source

Derived from Illumina 16S rRNA amplicon profiles from the Ravel-led UMB-HMP longitudinal vaginal cohort. Exact graph edges, sample metadata, feature screening results, and provenance are distributed under inst/extdata/hmp_gc/.

Details

Taxonomic count features detected in at least one percent of the retained HMP samples are converted to relative abundance and represented by ten principal components. A symmetric k = 3 nearest-neighbor graph is built in that representation, and the largest connected component is retained.

Examples

data(hmp.gc)
length(hmp.gc$adj_list)
#> [1] 4391
hmp.gc$graph_info[c("assay", "graph_constructor", "selected_k")]
#> $assay
#> [1] "Illumina 16S rRNA amplicon sequencing"
#> 
#> $graph_constructor
#> [1] "symmetric k-nearest-neighbor graph"
#> 
#> $selected_k
#> [1] 3
#>