Get pathways ranked on relevance from INDRA DB

Usage

getPathwaysFromIndra(
  annotated_df,
  main_target = "MEN1_HUMAN",
  target_type = "Protein"
)

Arguments

annotated_df: output of groupComparison function's comparisionResult table, which contains a list of proteins and their corresponding p-values, logFCs, along with additional HGNC ID and HGNC name columns
main_target: A main target, e.g. main target of a drug or protein of particular interest
target_type: One of either 'Protein' or 'Drug'. Default is 'Protein'

Value

df of pathways

Examples

annotated_df <- data.table::fread(system.file(
    "extdata/groupComparisonModel.csv",
    package = "MSstatsBioNet"
))
pathways <- getPathwaysFromIndra(annotated_df, "P05067")
head(pathways)
#> $nodes
#>       id     logFC     pvalue hgncName
#> 7 P05067 0.7360012 0.02030666      APP
#> 
#> $edges
#>   source target
#> 1 P05067 P05067
#>                                                                        interaction
#> 1 Activation, Complex, Inhibition, IncreaseAmount, DecreaseAmount, Phosphorylation
#>   evidenceCount     logFC      prob
#> 1          2772 0.7360012 0.4862613
#>                                                                               evidenceLink
#> 1 https://db.indra.bio/statements/from_agents?subject=620@HGNC&object=620@HGNC&format=html
#>