cytoScapeMap: Generate cytoscape map files from peakTable

In WMBEdmands/MetMSLine: an automated and fully integrated pipeline for rapid processing of high-resolution LC-MS metabolomic datasets.

Description

Generate cytoscape map files from peakTable

Usage

cytoScapeMap(peakTable = NULL, obsNames = NULL, outDir = NULL,
  EICnos = NULL, fileNameId = "", corrThresh = 0.6,
  corrMethod = "spearman", delta = 0.05, MTC = "BH")

Arguments

peakTable	either a data.frame, full file path as a character string to a .csv file of a peak table in the form observation (samples) in columns and variables (Mass spectral signals) in rows. If argument is not supplied a GUI file selection window will open and a .csv file can be selected.
obsNames	character vector of observation (i.e. sample/ QC/ Blank) names to identify appropriate observation (sample) columns.
outDir	character full path of cytoscape file output directory. The function will create an additional subdirectory within this output called "cytoScapeFiles" into which files will be saved.
EICnos	character name of column in peakTable of unique feature numbers. This unique number (e.g. extracted ion chromatogram number) will be used to merge the peak table with the node attributes file.
fileNameId	character additional identificatory character string to add to the cytoscape output file names. default = "". e.g. "blankSubtracted" or "filtered".
corrThresh	correlation coefficient threshold to group features within a retention time cluster.
corrMethod	character correlation method see cor for details. default "spearman".
delta	numeric maximum p-value (following multiple testing correction) above which the null hypothesis (no correlation) is rejected.
MTC	character Multiple Testing Correction default is "BH", see p.adjust.methods for details of options. ("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"). Any p-values after multiple testing correction above the value of delta will have their corresponding correlation coefficents replaced with zero.

Value

writes 3 text files: network (.sif), node and edge attribute files as plain text (.txt) files in the output directory (see outDir).

WMBEdmands/MetMSLine documentation built on May 9, 2019, 10:03 p.m.