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Get subnetwork from INDRA database

getSubnetworkFromIndra.Rd

Using differential abundance results from MSstats, this function retrieves a subnetwork of protein interactions from INDRA database.

Usage

getSubnetworkFromIndra(
  input,
  protein_level_data = NULL,
  pvalueCutoff = NULL,
  statement_types = c("IncreaseAmount", "DecreaseAmount"),
  paper_count_cutoff = 1,
  evidence_count_cutoff = 1,
  correlation_cutoff = 0.3
)

Arguments

input

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

protein_level_data

output of the dataProcess function's ProteinLevelData table, which contains a list of proteins and their corresponding abundances. Used for annotating correlation information and applying correlation cutoffs.

pvalueCutoff

p-value cutoff for filtering. Default is NULL, i.e. no filtering

statement_types

list of interaction types to filter on. Equivalent to statement type in INDRA. Default is c("IncreaseAmount", "DecreaseAmount").

paper_count_cutoff

number of papers to filter on. Default is 1.

evidence_count_cutoff

number of evidence to filter on for each paper. E.g. A paper may have 5 sentences describing the same interaction vs 1 sentence. Default is 1.

correlation_cutoff

if protein_level_abundance is not NULL, apply a cutoff for edges with correlation less than a specified cutoff. Default is 0.3

Value

list of 2 data.frames, nodes and edges

Examples

input <- data.table::fread(system.file(
    "extdata/groupComparisonModel.csv",
    package = "MSstatsBioNet"
))
subnetwork <- getSubnetworkFromIndra(input)
#> Warning: NOTICE: This function includes third-party software components
#>         that are licensed under the BSD 2-Clause License. Please ensure to
#>         include the third-party licensing agreements if redistributing this
#>         package or utilizing the results based on this package.
#>         See the LICENSE file for more details.
head(subnetwork$nodes)
#>       id     logFC     pvalue hgncName
#> 3 O60313 0.9299641 0.01958418     OPA1
#> 7 P05067 0.7360012 0.02030666      APP
#> 8 P05090 0.5683951 0.01371505     APOD
head(subnetwork$edges)
#>   source target    interaction evidenceCount paperCount
#> 1 P05067 O60313 DecreaseAmount             5          2
#> 2 P05067 P05090 IncreaseAmount             1          1
#>                                                                                evidenceLink
#> 1 https://db.indra.bio/statements/from_agents?subject=620@HGNC&object=8140@HGNC&format=html
#> 2  https://db.indra.bio/statements/from_agents?subject=620@HGNC&object=612@HGNC&format=html