Calculate Product-Substrate Ratios

Calculate the ratio between the motif quantification of enzyme products and substrates for glycosyltransferases and sulfotransferases. For glycoproteomics data, ratios are calculated independently for each glycosite.

Usage

product_substrate_ratio(exp, enzymes)

Arguments

exp

A glyexp::GlycomicSE() or glyexp::GlycoproteomicSE() object.

enzymes

A character vector of glycosyltransferase or sulfotransferase names, or a list of their enzyme() objects. Starter glycosyltransferases are not supported because their substrates are not glycans.

Value

A plain SummarizedExperiment::SummarizedExperiment() with a product_substrate_ratio assay. For glycomics data, rowData() contains enzyme. For glycoproteomics data, it contains enzyme, protein, and protein_site. colData() and metadata are preserved from exp.

Details

Each rule contributes its product and acceptor motif once. Quantifications are summed across all rules of an enzyme before division, including when multiple rules contain the same motif. Rule rejects and requires are ignored. Ratios with zero substrate quantification are returned as NA.

Motifs are matched strictly for intact glycan structures and leniently for partial or reduced structures, consistent with other glyenzy motif-based functions.

References

Bao B, Kellman BP, Chiang AWT, et al. (2021). Correcting for sparsity and interdependence in glycomics by accounting for glycan biosynthesis. Nature Communications, 12, 4988. doi:10.1038/s41467-021-25183-5

Examples

exp <- glyexp::real_experiment2[seq_len(10), seq_len(3)]
#> Warning: replacing previous import ‘S4Arrays::makeNindexFromArrayViewport’ by ‘DelayedArray::makeNindexFromArrayViewport’ when loading ‘SummarizedExperiment’
product_substrate_ratio(exp, "ST6GAL1")
#> class: SummarizedExperiment 
#> dim: 1 3 
#> metadata(2): exp_type glycan_type
#> assays(1): product_substrate_ratio
#> rownames(1): ST6GAL1
#> rowData names(1): enzyme
#> colnames(3): S1 S2 S3
#> colData names(1): group