FSA_msp2Cytoscape {IDSL.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, 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)
##