data-funs {FELLA} | R Documentation

## Parse, build and load the KEGG knowledge model

### Description

Function `buildGraphFromKEGGREST` makes use of the KEGG REST API (requires internet connection) to build and return the curated KEGG graph.

Function `buildDataFromGraph` takes as input the KEGG graph generated by `buildGraphFromKEGGREST` and writes the KEGG knowledge model in the desired permanent directory.

Function `loadKEGGdata` loads the internal files containing the KEGG knowledge model into a `FELLA.DATA` object.

In general, `generateGraphFromKEGGREST` and `generateDataFromGraph` are one-time executions for a given organism and knowledge model, in this precise order. On the other hand, the user needs to run `loadKEGGdata` in every new R session to load such model into a `FELLA.DATA` object.

### Usage

    buildGraphFromKEGGREST(organism = "hsa", filter.path = NULL)

    buildDataFromGraph(keggdata.graph = NULL, databaseDir = NULL,
        internalDir = TRUE, matrices = c("hypergeom", "diffusion",
        "pagerank"), normality = c("diffusion", "pagerank"),
        dampingFactor = 0.85, niter = 100)

    loadKEGGdata(databaseDir = tail(listInternalDatabases(), 1),
        internalDir = TRUE, loadMatrix = NULL)

### Arguments

`organism` | Character, KEGG code for the organism of interest
`filter.path` | Character vector, pathways to filter. This is a pattern matched using regexp. E.g: `"01100"` to filter the overview metabolic pathway in any species
`keggdata.graph` | An igraph object generated by the function `buildGraphFromKEGGREST`
`databaseDir` | Character containing the directory to save KEGG files. It is a relative directory inside the library location if `internalDir = TRUE`. If left to `NULL`, an automatic name containing the date, organism and the KEGG release is generated.
`internalDir` | Logical, should the directory be internal in the package directory?
`matrices` | A character vector, containing any of these: `"hypergeom"`, `"diffusion"`, `"pagerank"`
`normality` | A character vector, containing any of these: `"diffusion"`, `"pagerank"`
`dampingFactor` | Numeric value between 0 and 1 (none inclusive), damping factor `d` for PageRank (`page.rank`)
`niter` | Numeric value, number of iterations to estimate the p-values for the CC size. Between 10 and 1e3.
`loadMatrix` | Character vector to choose if heavy matrices should be loaded. Can contain: `"diffusion"`, `"pagerank"`

### Details

In function `buildGraphFromKEGGREST`, The user specifies (i) an organism, and (ii) patterns matching pathways that should not be included as nodes. A graph object, as described in [Picart-Armada, 2017], is built from the comprehensive KEGG database [Kanehisa, 2017]. As described in the main vignette, accessible through `browseVignettes("FELLA")`, this graph has five levels that represent categories of KEGG nodes. From top to bottom: pathways, modules, enzymes, reactions and compounds. This knowledge representation is resemblant to the one formerly used by MetScape [Karnovsky, 2011], in which enzymes connect to genes instead of modules and pathways. The necessary KEGG annotations are retrieved through KEGGREST R package [Tenenbaum, 2013]. Connections between pathways/modules and enzymes are inferred through organism-specific genes, i.e. an edge is added if a gene connects both entries. However, in order to enrich metabolomics data, the user has to pass the graph object to `buildDataFromGraph` to obtain the `FELLA.USER` object. All the networks are handled with the igraph R package [Csardi, 2006].

Using `buildDataFromGraph` is the second step to use the `FELLA` package. The knoledge graph is used to compute other internal variables that are required to run any enrichment. The main point behind the enrichment is to provide a small part of the knowledge graph relevant to the supplied metabolites. This is accomplished through diffusion processes and random walks, followed by a statistical normalisation, as described in [Picart-Armada, 2017]. When building the internal files, the user can choose whether to store (i) matrices for each provided method, and (ii) vectors derived from such matrices to use the parametric approaches. These are optional but enable (i) faster permutations and custom metabolite backgrounds, and (ii) parametric approaches. WARNING: diffusion and PageRank matrices in (i) can allocate up to 250MB each. On the other hand, the `niter` parameter controls the amount of trials to approximate the distribution of the connected component size under uniform node sampling. For further info, see the option `thresholdConnectedComponent` in the details from `?generateResultsGraph`. Regarding the destination, the user can specify the name of the directory. Otherwise a name containing the creation date, the organism and the KEGG release will be used. The database can be stored within the library path or in a custom location.

Function `loadKEGGdata` returns a `FELLA.DATA` object from any of the databases generated by `FELLA.DATA`. This object is the starting point of any enrichment using `FELLA`. In case the user built the matrices for "diffusion" and "pagerank", he or she can choose to load them. Further detail on the methods can be found in [Picart-Armada, 2017]. The matrices allow a faster computation and the definition of a custom background, but use up to 250MB of memory each.

### Value

`buildGraphFromKEGGREST` returns the curated KEGG graph (class igraph)

`buildDataFromGraph` returns `invisible(TRUE)` if successful. As a side effect, the directory `outdir` is created, containing the internal data.

`loadKEGGdata` returns the `FELLA.DATA` object that contains the KEGG knowledge representation.

### References

Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y., & Morishima, K. (2017). KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic acids research, 45(D1), D353-D361.

Karnovsky, A., Weymouth, T., Hull, T., Tarcea, V. G., Scardoni, G., Laudanna, C., ... & Athey, B. (2011). Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data. Bioinformatics, 28(3), 373-380.

Tenenbaum, D. (2013). KEGGREST: Client-side REST access to KEGG. R package version, 1(1).

Chang, W., Cheng, J., Allaire, JJ., Xie, Y., & McPherson, J. (2017). shiny: Web Application Framework for R. R package version 1.0.5. https://CRAN.R-project.org/package=shiny

Picart-Armada, S., Fernandez-Albert, F., Vinaixa, M., Rodriguez, M. A., Aivio, S., Stracker, T. H., Yanes, O., & Perera-Lluna, A. (2017). Null diffusion-based enrichment for metabolomics data. PLOS ONE, 12(12), e0189012.

### See Also

class `FELLA.DATA`

### Examples

    ## Toy example
    ## In this case, the graph is not built from current KEGG.
    ## It is loaded from sample data in FELLA
    data("FELLA.sample")
    ## Graph to build the database (this example is a bit hacky)
    g.sample <- FELLA:::getGraph(FELLA.sample)
    dir.tmp <- paste0(tempdir(), "/", paste(sample(letters), collapse = ""))
    ## Build internal files in a temporary directory
    buildDataFromGraph(
    keggdata.graph = g.sample,
    databaseDir = dir.tmp,
    internalDir = FALSE,
    matrices = NULL,
    normality = NULL,
    dampingFactor = 0.85,
    niter = 10)
    ## Load database
    myFELLA.DATA <- loadKEGGdata(
    dir.tmp,
    internalDir = FALSE)
    myFELLA.DATA

    ######################

    ## Not run:
    ## Full example

    ## First step: graph for Mus musculus discarding the mmu01100 pathway
    ## (an analog example can be built from human using organism = "hsa")
    g.mmu <- buildGraphFromKEGGREST(
    organism = "mmu",
    filter.path = "mmu01100")
    summary(g.mmu)
    cat(comment(g.mmu))

    ## Second step: build internal files for this graph
    ## (consumes some time and memory, especially if we compute
    "diffusion" and "pagerank" matrices)
    buildDataFromGraph(
    keggdata.graph = g.mmu,
    databaseDir = "example_db_mmu",
    internalDir = TRUE,
    matrices = c("hypergeom", "diffusion", "pagerank"),
    normality = c("diffusion", "pagerank"),
    dampingFactor = 0.85,
    niter = 1e3)
    ## Third step: load the internal files into a FELLA.DATA object
    FELLA.DATA.mmu <- loadKEGGdata(
    "example_db_mmu",
    internalDir = TRUE,
    loadMatrix = c("diffusion", "pagerank"))
    FELLA.DATA.mmu

    ## End(Not run)

[Package FELLA version 1.2.0 Index]