FSA_msp2Cytoscape: FSA Cytoscape Files Generator

In IDSL.FSA: Fragmentation Spectra Analysis (FSA)

FSA Cytoscape Files Generator

Description

This function generates necessary files from pairwise MSP blocks analysis to create Cytoscape networks.

Usage

FSA_msp2Cytoscape(path, MSPfile = "", mspVariableVector = NULL,
mspNodeID = NULL, massError = 0.01, RTtolerance = NA, minEntropySimilarity = 0.75,
allowedNominalMass = FALSE, allowedWeightedSpectralEntropy = TRUE,
noiseRemovalRatio = 0.01, number_processing_threads = 1)

Arguments

path	address of .msp file or an FSDB
MSPfile	name of .msp file
mspVariableVector	a vector of msp variables
mspNodeID	msp Node ID which is the ID that is required for the ‘specsim’ ID generation
massError	Mass accuracy in Da
RTtolerance	Retention time tolerance (min) to match msp blocks. Select NA to ignore retention time match. This option is so helpful to find co-occurring compounds.
minEntropySimilarity	Minimum entropy similarity score
allowedNominalMass	c(TRUE, FALSE). Select 'TRUE' only for nominal mass analysis.
allowedWeightedSpectralEntropy	c(TRUE, FALSE). Weighted entropy to measure entropy similarity score.
noiseRemovalRatio	noise removal ratio relative to the basepeak to measure entropy similarity score (in percent)
number_processing_threads	Number of processing threads for multi-threaded processing

Value

node_attributes_dataFrame	node_attributes dataframe. A string to store using 'writeTable' function of R after a tab separation.
edge_dataFrame	edge dataframe. A string to store using the 'writeTable' function of R after a tab separation.
correlation_network	correlation_network dataframe. A string to store using the 'writeTable' function of R after a tab separation.
FSDB	Fragmentation spectra database (FSDB) object
exclusionMSPnoideid	A vector of MSP node ids which can be excluded to create a library of unique MSP blocks.
filteredNetworkSIF	A filtered network in the cytoscape SIF format that does not have redundant MSP blocks within a RT window.

References

Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B. and Ideker, T., (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research, 13(11), 2498-2504, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1101/gr.1239303")}

Examples

path_extdata <- system.file("extdata", package = "IDSL.FSA")
mspFileName <- "Kynurenine_Kynurenic_acid.msp"
##
listCytoscape <- FSA_msp2Cytoscape(path = path_extdata,
MSPfile = mspFileName, mspVariableVector = c("Name", "Collision_energy"),
mspNodeID = NULL, massError = 0.01, RTtolerance = NA, minEntropySimilarity = 0,
noiseRemovalRatio = 0, allowedNominalMass = FALSE,
allowedWeightedSpectralEntropy = TRUE, number_processing_threads = 1)
##
FSDB <- listCytoscape[["FSDB"]]
##
temp_wd <- tempdir() # just a temporary folder to save results
##
write.table(listCytoscape[["node_attributes_dataFrame"]], paste0(temp_wd,
"/node_attributes_dataFrame.txt"), quote = FALSE, sep = "\t", row.names = FALSE,
col.names = FALSE)
##
write.table(listCytoscape[["correlation_network"]], paste0(temp_wd,
"/correlation_network.sif"), quote = FALSE, sep = "\t", row.names = FALSE,
col.names = FALSE)
##
write.table(listCytoscape[["edge_dataFrame"]], paste0(temp_wd,
"/edge_dataFrame.txt"), quote = FALSE, sep = "\t", row.names = FALSE,
col.names = FALSE)
##

IDSL.FSA documentation built on July 9, 2023, 6:45 p.m.