filterSif: Keep interactions in SIF network based on certain criteria

In cannin/paxtoolsr: Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

Keep interactions in SIF network based on certain criteria

Description

Keep interactions in SIF network based on certain criteria

Usage

filterSif(
  sif,
  ids = NULL,
  interactionTypes = NULL,
  dataSources = NULL,
  interactionPubmedIds = NULL,
  pathwayNames = NULL,
  mediatorIds = NULL,
  edgelist = NULL,
  idsBothParticipants = FALSE,
  edgelistCheckReverse = TRUE,
  verbose = FALSE
)

Arguments

sif	a binary SIF as a data.frame with three columns: "PARTICIPANT_A", "INTERACTION_TYPE", "PARTICIPANT_B"
ids	a vector of IDs to be kept
interactionTypes	a vector of interaction types to be kept (List of interaction types: http://www.pathwaycommons.org/pc2/formats)
dataSources	a vector of data sources to be kept. For Extended SIF.
interactionPubmedIds	a vector of Pubmed IDs to be kept. For Extended SIF.
pathwayNames	a vector of pathway names to be kept. For Extended SIF.
mediatorIds	a vector of mediator IDs to be kept. For Extended SIF. Mediator IDs are the full BioPAX objects that were simplified to interaction given in the SIF. For Extended SIF.
edgelist	a two-column data.frame where each row is an interaction to be kept. Directionality is ignored (e.g. Edge A B will return interactions A B and B A from SIF)
idsBothParticipants	a boolean whether both interaction participants should be in a given interaction when using the ids parameter; TRUE if both (DEFAULT: TRUE)
edgelistCheckReverse	a boolean whether to check for edges in the reverse order (DEFAULT: TRUE)
verbose	Show debugging information (DEFAULT: FALSE)

Value

filtered interactions with three columns: "PARTICIPANT_A", "INTERACTION_TYPE", "PARTICIPANT_B". The intersection of multiple filters is returned.

Examples

results <- readSif(system.file("extdata", "test_sif.txt", package="paxtoolsr"))
intTypes <- c("controls-state-change-of", "controls-expression-of", "catalysis-precedes")
filteredNetwork <- filterSif(results, intTypes)

tmp <- readSifnx(system.file("extdata", "test_sifnx_250.txt", package = "paxtoolsr"))
results <- filterSif(tmp$edges, ids=c("CHEBI:17640", "MCM3"))
results <- filterSif(tmp$edges, dataSources=c("INOH", "KEGG"))
results <- filterSif(tmp$edges, dataSources=c("IntAct"), ids=c("CHEBI:17640", "MCM3"))
results <- filterSif(tmp$edges, pathwayNames=c("Metabolic pathways"))
results <- filterSif(tmp$edges, 
  mediatorIds=c("http://purl.org/pc2/8/MolecularInteraction_1452626895158"))
results <- filterSif(tmp$edges, interactionPubmedId="17654400")

tmp <- readSifnx(system.file("extdata", "test_sifnx_250.txt", package = "paxtoolsr"))
edgelist <- read.table(system.file("extdata", "test_edgelist.txt", package = "paxtoolsr"), 
  sep="\t", header=FALSE, stringsAsFactors=FALSE)
results <- filterSif(tmp$edges, edgelist=edgelist)

cannin/paxtoolsr documentation built on Feb. 2, 2023, 11:44 a.m.