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Validate arguments passed to validateCreateEnrichMapMultiComplex() function

Source: R/methodsEmapInternal.R
validateCreateEnrichMapMultiComplexAsIgraphArg.Rd

Validate the arguments passed to validateCreateEnrichMapMultiComplex() function. First, the object containing the enrichment results must correspond to a object created by gprofiler2 software. Second, the selected source must at least have one enriched term in the results. Then, if the source is 'TERM_ID', the listed terms must be present in the enrichment results.

Usage

validateCreateEnrichMapMultiComplexAsIgraphArg(
  gostObjectList,
  queryInfo,
  showCategory,
  similarityCutOff = similarityCutOff
)

Arguments

gostObjectList

a list of gprofiler2 objects that contain the results from an enrichment analysis. The list must contain at least 2 entries. The number of entries must correspond to the number of entries for the queryList parameter.

queryInfo

a data.frame contains one row per group being displayed. The number of rows must correspond to the number of entries for the gostObjectList parameter. The mandatory columns are:

  • queryName: a character string representing the name of the query retained for this group). The query names must exist in the associated gostObjectList objects and follow the same order.

  • source: a character string representing the selected source that will be used to generate the network. To hand-pick the terms to be used, "TERM_ID" should be used and the list of selected term IDs should be passed through the termIDs parameter. The possible sources are "GO:BP" for Gene Ontology Biological Process, "GO:CC" for Gene Ontology Cellular Component, "GO:MF" for Gene Ontology Molecular Function, "KEGG" for Kegg, "REAC" for Reactome, "TF" for TRANSFAC, "MIRNA" for miRTarBase, "CORUM" for CORUM database, "HP" for Human phenotype ontology and "WP" for WikiPathways. Default: "TERM_ID".

  • removeRoot: a logical that specified if the root terms of the selected source should be removed (when present).

  • termIDs: a character strings that contains the term IDS retained for the creation of the network separated by a comma ',' when the "TERM_ID" source is selected. Otherwise, it should be a empty string ("").

  • groupName: a character strings that contains the name of the group to be shown in the legend. Each group has to have a unique name.

showCategory

a positive integer or NULL. If a integer, the first n terms will be displayed. If NULL, all terms will be displayed.

similarityCutOff

a positive numeric, larger than zero and small than 1 that represent the minimum similarity level between two nodes (terms) to be linked by an edge.

Value

TRUE when all arguments are valid

Author

Astrid Deschênes

Examples


## Load the result of an enrichment analysis done with gprofiler2
data(parentalNapaVsDMSOEnrichment)
data(rosaNapaVsDMSOEnrichment)

queryDataFrame <- data.frame(queryName=c("parental_napa_vs_DMSO", 
    "rosa_napa_vs_DMSO"), source=c("KEGG", "WP"), removeRoot=c(TRUE, TRUE),
    termIDs=c("", ""), groupName=c("parental - KEGG", "rosa - WP"), 
    stringsAsFactors=FALSE)

## Check that all arguments are valid
enrichViewNet:::validateCreateEnrichMapMultiComplexAsIgraphArg(
    gostObjectList=list(parentalNapaVsDMSOEnrichment, 
                            rosaNapaVsDMSOEnrichment),
    queryInfo=queryDataFrame, showCategory=20, similarityCutOff=0.2)
#> [1] TRUE