Get subnetwork from INDRA database

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

Usage

getSubnetworkFromIndra(input, pvalueCutoff = NULL)

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

pvalueCutoff

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

Value

list of 2 data.frames, nodes and edges

Examples

input <- data.table::fread(system.file(
    "extdata/groupComparisonModel.csv",
    package = "MSstatsBioNet"
))
subnetwork <- getSubnetworkFromIndra(input, pvalueCutoff = 0.05)
#> 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$nodes)
#> [1] id     logFC  pvalue
#> <0 rows> (or 0-length row.names)
head(subnetwork$edges)
#> [1] source        target        interaction   evidenceCount evidenceLink 
#> <0 rows> (or 0-length row.names)