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Simulated Expression Matrix for WSS Examples

Source: R/data.R
wss_example_expression.Rd

A small, fully simulated samples-by-proteins matrix for trying out calculate_WSS(). Its columns are the 887 proteins (gene symbols) that survive the default deduplication and module-size filter of the bundled "core_AD_plasma_biomarkers" reference set, so calculate_WSS(wss_example_expression) scores all 75 modules without warnings. Values are on a z-score-like scale, as expected for normalized input.

Usage

wss_example_expression

Format

A numeric matrix with 50 rows (samples, named sample01 to sample50) and 887 columns (proteins, named by gene symbol).

Source

Simulated; see data-raw/simulate_examples.R in the package source.

Details

Each module was given a latent per-sample factor, and its proteins load on that factor in the direction of their mean_beta, plus independent noise. The data are random draws and contain no participant data; they carry no biological meaning and are for demonstration only.

See also

calculate_WSS(), wss_example_biomarkers

Examples

dim(wss_example_expression)
#> [1]  50 887
res <- calculate_WSS(wss_example_expression)
head(res$scores[, 1:3])
#>          Merged.M17   Merged.M7   Merged.M4
#> sample01 -0.8723738  0.36490845  0.04891509
#> sample02  0.2344854 -0.50295921 -0.54133339
#> sample03  0.8852222 -0.41936437 -0.56949082
#> sample04  0.8491436  0.05028353 -0.97018547
#> sample05 -0.2620853 -1.56467707  0.53368294
#> sample06 -0.6801977 -1.26890805  0.48510968