Metabolic Preference Assay for Rapid Diagnosis of Bloodstream Infections

Authors: Thomas Rydzak, Ryan A. Groves, Ruichuan Zhang, Raied Aburashed, Rajnigandha Pushpker, Maryam Mapar, and Ian A. Lewis

MET is an R statistics-based utility tool that supports untargeted metabolomics analysis, visualization, and statistical analyses of LC-MS datasets. MET reads .csv format lists, in a format compatible with the MAVEN LC-MS data analysis software tool [ref].

METRead

Read in a Maven peak picked CSV file

METWrite

Write out a CSV file of the dataset

METStats

• This function takes a MAVEN pick picked format list and performances various statistical techinques
• inDat - METen format table
• rCst - Logical - TRUE clusters by row
• cCst - Logical - TRUE clusters by column
• pCst - Logical - TRUE ranks rows by P value
• nCst - Logical - TRUE sorts samples by name
• grid - Logical - TRUE plots the a sample grid over the heatmap
• pca - Logical - TRUE makes the PCA plots
• linePlot - Logical - TRUE makes a line plot
• stackPlot - Logical - TRUE makes a staked line plot
• heatMap - Logical - TRUE makes a classic heatmap
• barPlot - Logical - Plots bar figure, note this needs replicates see "by"
• zPlot - Logical - this plots data relative to a reference sample set
• scale - controls how data are normalized must be one of the following: "log", "durbin", "row", "column", or "none"
  • 'log' applies base 2 log transform
  • 'durbin' applies durbin transform
  • 'row' normalizes by row
  • 'column' noralizes by column
  • 'zScore' normalizes relative to a control, sets equal variance
  • 'none' does not apply any normalization
• c - integer - constant for durbin trasform (0 is ln)
• excludeName - character, names of columns to be excluded from analysis
• na.rm - Logical - TRUE converts NA to 0, INF to positive max, -INF to negative max
• avgRep - logical, returns the mean intensity for each group
• sdRep - logical, returns the standard deviation for each group note, avgRep and sdRep cannont be both set to T
• inverse - logical, inverts the incoming data (1/data)
• pThresh - logical - excludes data above the pValue threshold
• returnMeta - Logical, if T, will return all input meta data note: this cannot be used with column/p clustering or thresholding
• rmZero - logical - removes rows with all zero intensities

METPlot

• This function takes a MAVEN pick picked format list and makes several types of plots
• inDat - METen format table
• grid - Logical - TRUE plots the a sample grid over the heatmap
• pca - Logical - TRUE makes the PCA plots
• linePlot - Logical - TRUE makes a line plot
• stackPlot - Logical - TRUE makes a staked line plot
• heatMap - Logical - TRUE makes a classic heatmap
• barPlot - Logical - Plots bar figure, note this needs replicates see "by"
• zPlot - Logical - this plots data relative to a reference sample set
• scale - controls how data are normalized must be one of the following: "log", "durbin", "row", "column", or "none"
  • 'log' applies base 2 log transform
  • 'durbin' applies durbin transform
  • 'row' normalizes by row
  • 'column' noralizes by column
  • 'zScore' normalizes relative to a control, sets equal variance
  • 'none' does not apply any normalization
• c - integer - constant for durbin trasform (0 is ln)
• excludeName - character, names of columns to be excluded from analysis
• n - number of levels used in heatmap
• zlim - numeric vector of length 2 for the c(min, max) plotted value, if zlim is missing or NULL, then all data are plotted
• logScale - logical - TRUE uses log2 intervals and disable n
• byClass - Logical - TRUE agregates data according to values in the 'notes' column
• excludeName - character, names of columns to be excluded from analysis
• na.rm - Logical - TRUE converts NA to 0, INF to positive max, -INF to negative max
• returnPCA - logical - TRUE returnes PCA scores
• zJitter - Logical, if true will offset the x scale for zPlots
• returns the dataframe used to plot the data

METCluster

• Function for clustering untargeted mz data
• mzTable - dataframe - METen format dataframe from untargeted csv METen output
• mzThresh - numeric - Mass tolerance in ppm
• rtThresh - numeric - Renention time tolerance in minutes
• pW - numeric vector, 0 to 1 - weight given to mass,retention time, and correlation
• pThresh - numeric, 0 to 1 - overall probablility threshold
• adList - numeric vector - list of known adducts
• collapse - logical - T collapses groups to highest intensity signal
• clusterOnly - logical - T returns collapsed groups with multiple signals