Reduce redundancy of human GO terms

This function will reduce GO redundancy first by creating a semantic similarity matrix (using GOSemSim::mgoSim), which is then passed through rrvgo::reduceSimMatrix(), which will reduce a set of GO terms based on their semantic similarity and scores (in this case, a default score based on set size is assigned.)

go_reduce(
  pathway_df,
  orgdb = "org.Hs.eg.db",
  threshold = 0.7,
  scores = NULL,
  measure = "Wang"
)

Arguments

pathway_df	a `data.frame` or tibble object, with the following columns: `go_type`: the sub-ontology the GO term relates to. Should be one of `c("BP", "CC", "MF")`. `go_id`: the gene ontology identifier (e.g. GO:0016209)
orgdb	`character()` vector, indicating name of the org.* Bioconductor package to be used
threshold	`numeric()` vector. Similarity threshold (0-1) for `rrvgo::reduceSimMatrix()`. Default option is 0.7. Some guidance: For large term groupings, use `threshold = 0.9` For medium term groupings, use `threshold = 0.7` For small term groupings, use `threshold = 0.5` For tiny term groupings, use `threshold = 0.4`
scores	named vector, with scores (weights) assigned to each term. Higher is better. Can be NULL (default, means no scores. In this case, a default score based on set size is assigned, thus favoring larger sets). Note: if you have p-values as scores, consider log-transforming them (`-log10(p)`).
measure	`character()` vector, indicating method to be used to calculate semantic similarity measure. Must be one of the methods supported by GOSemSim: c("Resnik", "Lin", "Rel", "Jiang", "Wang"). Default is "Wang".

Value

a tibble object of pathway results, a "reduced" parent term to which pathways have been assigned. New columns:

parent_id: the GO ID of the parent term
parent_term: a description of the GO ID
parent_sim_score: the similarity score between the child GO term and its parent term

Details

Semantic similarity is calculated using the "Wang" method, a graph-based strategy to compute semantic similarity using the topology of the GO graph structure. GOSemSim::mgoSim does permit use of other measures (primarily information-content measures), but "Wang" is used as the default in GOSemSim (and was, thus, used as the default here). If you wish to use a different measure, please refer to the GOSemSim documentation.

rrvgo::reduceSimMatrix() creates a distance matrix, defined as (1-simMatrix). The terms are then hierarchically clustered using complete linkage (an agglomerative, or "bottom-up" clustering approach), and the tree is cut at the desired threshold. The term with the highest "score" is used to represent each group.

References

Yu et al. (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics (Oxford, England), 26:7 976--978, April 2010. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976 PMID: 20179076
Yu (2021) Biomedical Knowledge Mining using GOSemSim and clusterProfiler https://yulab-smu.top/biomedical-knowledge-mining-book/index.html
Sayols S (2020). rrvgo: a Bioconductor package to reduce and visualize Gene Ontology terms. https://ssayols.github.io/rrvgo

Examples

file_path <-
    system.file(
        "testdata",
        "go_test_data.txt",
        package = "rutils",
        mustWork = TRUE
    )

pathway_df <-
    readr::read_delim(file_path,
        delim = "\t"
    )
#> 
#> ── Column specification ────────────────────────────────────────────────────────
#> cols(
#>   go_type = col_character(),
#>   go_id = col_character(),
#>   go_term = col_character()
#> )

go_reduce(
    pathway_df = pathway_df,
    orgdb = "org.Hs.eg.db",
    threshold = 0.9,
    scores = NULL,
    measure = "Wang"
)
#> [1] "Reducing sub-ontology: BP"
#> preparing gene to GO mapping data...
#> No scores provided. Falling back to term's size
#> # A tibble: 10 x 6
#>    go_type go_id   go_term          parent_id parent_sim_score parent_term      
#>    <chr>   <chr>   <chr>            <chr>                <dbl> <chr>            
#>  1 BP      GO:001… Regulation of n… GO:00109…            1     regulation of ne…
#>  2 BP      GO:006… Axon development GO:00109…            0.618 regulation of ne…
#>  3 BP      GO:005… Negative regula… GO:00109…            0.408 regulation of ne…
#>  4 BP      GO:000… Ensheathment of… GO:00109…            0.304 regulation of ne…
#>  5 BP      GO:002… Regulation of c… GO:00226…            1     regulation of ce…
#>  6 BP      GO:009… Regulation of t… GO:00226…            0.169 regulation of ce…
#>  7 BP      GO:005… Synapse organiz… GO:00508…            1     synapse organiza…
#>  8 BP      GO:007… Neuron death     GO:00508…            0.227 synapse organiza…
#>  9 BP      GO:005… Establishment o… GO:00508…            0.156 synapse organiza…
#> 10 BP      GO:003… Cytoskeleton-de… GO:00508…            0.134 synapse organiza…

Arguments

Value

Details

References

See also

Examples