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,
  protein_level_data = NULL,
  pvalueCutoff = NULL,
  statement_types = c("IncreaseAmount", "DecreaseAmount"),
  paper_count_cutoff = 1,
  evidence_count_cutoff = 1,
  correlation_cutoff = 0.3,
  sources_filter = NULL,
  logfc_cutoff = NULL,
  force_include_proteins = NULL,
  force_include_other = 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

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

sources_filter

filtering only on specific sources. Default is no filter, i.e. NULL. Otherwise, should be a list, e.g. c('reach', 'medscan').

logfc_cutoff

absolute log fold change cutoff for filtering proteins. Only proteins with |logFC| greater than this value will be retained. Default is NULL, i.e. no logFC filtering.

force_include_proteins

character vector of protein identifiers to exempt from all filtering steps. These proteins will be retained regardless of p-value, logFC, or other filtering criteria. Default is NULL, i.e. no exemptions.

force_include_other

character vector of identifiers to include in the network, regardless if those ids are in the input data. Should be formatted as "namespace:identifier", e.g. "HGNC:1234" or "CHEBI:4911".

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$nodes)
#>        id hgncName   Site      logFC  adj.pvalue
#>    <char>   <char> <char>      <num>       <num>
#> 1: O60313     OPA1   <NA>  0.9299641 0.019584180
#> 2: P05067      APP   <NA>  0.7360012 0.020306662
#> 3: P05090     APOD   <NA>  0.5683951 0.013715050
#> 4: P05362    ICAM1   <NA> -2.0222933 0.001635934
head(subnetwork$edges)
#>   source target site    interaction evidenceCount paperCount
#> 1 P05067 O60313 <NA> DecreaseAmount             6          2
#> 2 P05067 P05090 <NA> IncreaseAmount             2          1
#> 3 P05067 P05362 <NA> IncreaseAmount             3          1
#> 4 O60313 P05067 <NA> DecreaseAmount             1          1
#> 5 P05067 O60313 <NA> 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
#> 3 https://db.indra.bio/statements/from_agents?subject=620@HGNC&object=5344@HGNC&format=html
#> 4 https://db.indra.bio/statements/from_agents?subject=8140@HGNC&object=620@HGNC&format=html
#> 5 https://db.indra.bio/statements/from_agents?subject=620@HGNC&object=8140@HGNC&format=html
#>   sourceCounts
#> 1 {"reach": 3}
#> 2 {"reach": 2}
#> 3 {"reach": 3}
#> 4 {"reach": 1}
#> 5 {"reach": 1}