filterSif: Keep interactions in SIF network based on certain criteria

In paxtoolsr: PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons

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)

paxtoolsr documentation built on Nov. 8, 2020, 8:29 p.m.