paxtoolsr (version 1.6.3)

filterSif: Keep interactions in SIF network based on certain criteria

Description

Keep interactions in SIF network based on certain criteria

Usage

filterSif(sif, interactionTypes = NULL, dataSources = NULL, ids = NULL,
  edgelist = NULL)

Arguments

sif

a binary SIF as a data.frame with three columns: "PARTICIPANT_A", "INTERACTION_TYPE", "PARTICIPANT_B"

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

ids

a vector of IDs to be kept

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)

Value

• filtered interactions with three columns: "PARTICIPANT_A", "INTERACTION_TYPE", "PARTICIPANT_B". The intersection of multiple filters is returned. The return class is the same as the input: data.frame or data.table

concept

paxtoolsr

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$edges, dataSources=c("INOH", "KEGG"))
results <- filterSif(tmp$edges, ids=c("CHEBI:17640", "MCM3"))
results <- filterSif(tmp$edges, dataSources=c("IntAct"), ids=c("CHEBI:17640", "MCM3"))

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)