filterSif {paxtoolsr} | R Documentation |
Keep interactions in SIF network based on certain criteria
filterSif(sif, interactionTypes = NULL, dataSources = NULL, ids = NULL, edgelist = NULL)
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) |
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
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)