readSifnx: Read in a Extended SIF file

Description Usage Arguments Details Value Examples

View source: R/readSifnx.R

Description

Read in a Extended SIF file

Usage

1
readSifnx(inputFile, asDT = FALSE)

Arguments

inputFile

an inputFile

asDT

a boolean return file as a data.table (DEFAULT: FALSE)

Details

SIFNX files from Pathway Commons commonly come a single file that includes a tab-delimited sections for nodes and another for edges. The sections are separated by an empty lines. These sections must be split before they are read.

Value

a list with nodes and edges entries

Examples

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results <- readSifnx(system.file("extdata", "test_sifnx.txt", package="paxtoolsr"))
chebiIds <- lapply(results$nodesUniXref, function(x) { x[which(grepl("CHEBI", x))] })

cannin/paxtoolsr documentation built on Aug. 16, 2018, 1:18 a.m.