metabCombine: metabCombiner Wrapper Function

In hhabra/metabCombiner: Method for Combining LC-MS Metabolomics Feature Measurements

metabCombiner Wrapper Function

Description

metabCombine wraps the five main metabCombiner workflow steps into a single wrapper function. Parameter list arguments organize program parameters by constituent package functions.

Usage

metabCombine(
  xdata,
  ydata,
  binGap = 0.005,
  xid = NULL,
  yid = NULL,
  means = list(mz = FALSE, rt = FALSE, Q = FALSE),
  fitMethod = "gam",
  rtOrder = TRUE,
  union = FALSE,
  impute = FALSE,
  anchorParam = selectAnchorsParam(),
  fitParam = fitgamParam(),
  scoreParam = calcScoresParam(),
  labelParam = labelRowsParam()
)

Arguments

xdata	metabData object. One of two datasets to be combined.
ydata	metabData object. One of two datasets to be combined.
binGap	numeric parameter used for grouping features by m/z. See ?mzGroup for more details.
xid	character identifier of xdata. If xdata is a metabData, assigns a new ID for this dataset; if xdata is a metabCombiner, must be assigned to one of the existing dataset IDs. See details for more information.
yid	character identifier of ydata. If ydata is a metabData, assigns a new ID for this dataset; if ydata is a metabCombiner, must be assigned to one of the existing dataset IDs. See details for more information.
means	logical. Option to take average m/z, rt, and/or Q from metabComber. May be a vector (length = 3), single value (TRUE/FALSE), or a list with names "mz", "rt", "Q" as names.
fitMethod	RT spline-fitting method, either "gam" or "loess"
rtOrder	logical. If set to TRUE, retention order consistency expected when resolving conflicting alignments for metabCombiner object inputs.
union	logical. Option to include non-matched features in final combinedTable results
impute	logical. If TRUE, imputes the mean mz/rt/Q values for missing features in metabCombiner object inputs before use in alignment (not recommended for disparate data alignment); if FALSE, features with missing information are dropped.
anchorParam	list of parameter values for selectAnchors() function
fitParam	list of parameter values for fit_gam() or fit_loess()
scoreParam	list of parameter values for calcScores()
labelParam	list of parameter values for labelRows()

Details

The five main steps in metabCombine are 1) m/z grouping & combined table construction, 2) selection of ordered pair RT anchors, 3) nonlinear spline (Basis Spline GAM or LOESS) fitting to predict RTs, 4) score calculation and feature pair alignment ranking, 5) combined table row annotation and reduction. metabData arguments xdata & ydata and m/z grouping binGap are required for step 1.

Steps 2-5 are handled by anchors, fit, scores, & labels, respectively, with lists containing the argument values for each step expected for these arguments. selectAnchorsParam, fitgamParam, fitloessParam, calcScoresParam, & labelRowsParam load the default program values of selectAnchors, fit_gam, fit_loess, calcScores & labelRows, respectively. These program arguments should be modified as necessary for the datasets used for analysis.

By default, the RT fitting method (fitMethod) is set to "gam", which means the argument fit is a list of parameters for fit_gam; if the (fitMethod) argument is set to "loess", then the fit argument expects a list of fit_loess parameters.

Value

a metabCombiner object following complete analysis

See Also

selectAnchorsParam, fitgamParam, calcScoresParam, labelRowsParam, fitloessParam

Examples

data("plasma20")
data("plasma30")

p30 <- metabData(plasma30, samples = "CHEAR")
p20 <- metabData(plasma20, samples = "Red", rtmax = 17.25)

#parameter lists:
saParam <- selectAnchorsParam(tolrtq = 0.2, windy = 0.02, tolmz = 0.002)
fitParam <- fitgamParam(k = seq(12,15), iterFilter = 1, outlier = "boxplot",
                        family = "gaussian", prop = 0.6, coef = 1.5)
scoreParam <- calcScoresParam(A = 75, B = 15, C = 0.3)
labelParam <- labelRowsParam(maxRankX = 2, maxRankY = 2, delta = 0.1)

#metabCombine wrapper
p.combined <- metabCombine(xdata = p30, ydata = p20, binGap = 0.0075,
                           anchorParam = saParam, fitParam = fitParam,
                           scoreParam = scoreParam, labelParam = labelParam)

##to view results
p.combined.table <- combinedTable(p.combined)

hhabra/metabCombiner documentation built on June 5, 2024, 5:46 a.m.