Skip to contents

Perform metabolomics data analysis workflow

Source: R/metabolomics_computation.R
met.workflow.Rd

met.workflow runs a metabolomics analysis workflow, including univariate analysis (ANOVA) and multivariate analyses (PCA and PLS-DA) and creates a report with various graphical results.

Usage

met.workflow(
  mSetObj,
  rowNorm = "NULL",
  transNorm = "NULL",
  scaleNorm = "NULL",
  ref = NULL,
  norm.vec = NULL,
  contrast.type = "all",
  control = NULL,
  contrast = NULL,
  class_order = FALSE,
  alpha = 0.05,
  lfc = 2,
  posthoc_method = "tukey",
  nonpar = FALSE,
  permut.num = 500,
  vip.thresh = 1,
  volcano.test = "anova",
  volcano.add_names = TRUE,
  volcano.label_size = 3,
  volcano.adjusted = FALSE,
  pls.data = "all",
  pls.cv.method = "LOOCV",
  pls.cv.k = 5,
  plot = FALSE,
  export = FALSE,
  export.format = "pdf",
  dpi = 300,
  report = FALSE,
  report.dir = NULL,
  export.dir = "met.ProcessedData"
)

Arguments

mSetObj

Enter the name of the created mSet object (see met.read_data).

rowNorm

(Character) Select the option for row-wise normalization (see met.normalize for options).

transNorm

(Character) Select option to transform the data (see met.normalize for options).

scaleNorm

(Character) Select option for scaling the data (see met.normalize for options).

ref

(Character) Enter the name of the reference sample or the reference feature (if rowNorm = "GroupPQN", "SamplePQN", or "CompNorm".

norm.vec

(Numeric vector) Vector with sample-specific scaling factors. Only applicable for rowNorm = "SpecNorm".

contrast.type

(Character) Enter the type of contrast to be used for ANOVA analysis. Options are "all" (default), "control", or "manual".

control

(If contrast.type = "control") Enter the name of the control group (e.g. "Control") to be used for ANOVA analysis.

contrast

(If contrast.type = "manual") Enter a contrast or vector of contrasts to be used for ANOVA analysis. E.g.: "ConditionA_vs_ConditionB" or c("ConditionA_vs_ConditionB", "ConditionC_vs_ConditionD").

class_order

(Logical, TRUE or FALSE) Class order matters (i.e. implying time points, disease severity, etc.).

alpha

(Numeric) Enter significance threshold for adjusted p values (false discovery rate - FDR; for ANOVA with post-hoc analyses).

lfc

(Numeric) Enter relevance threshold for log2 fold changes in pair-wise comparisons (for ANOVA with post-hoc analyses).

posthoc_method

(Character) Enter the name of the ANOVA post-hoc test, "fisher" or "tukey".

nonpar

(Logical) Use a non-parametric ANOVA test (TRUE) or not (FALSE).

permut.num

(Numeric) Number of permutations in PLS-DA permutation tests.

vip.thresh

(Numeric) Enter a chosen relevance threshold for PLS-DA VIP scores.

volcano.test

(Character) Enter the name of the statistical, univariate analysis to perform, either "anova" or "ttest".

volcano.add_names

(Logical) Display compound labels next to dots within the volcano plot (TRUE) or not (FALSE).

volcano.label_size

(Numerical) Enter the font size of compound labels within the volcano plot (if volcano.add_names = TRUE)

volcano.adjusted

(Logical) Display adjusted p-values on y axis of the volcano plot (TRUE) or not (FALSE)? (only applicable to volcano.test = "ttest")

pls.data

(Character) Enter "all" to train the PLS(-DA) model on your whole (filtered and normalized) dataset or "anova" to use a subset of features defined as significant based on ANOVA analysis.

pls.cv.method

(Character) Enter one of two methods for PLS-DA model (cross) validation:

  • "LOOCV" performs leave-one-out cross validation

  • "CV" performs k-fold cross validation.

pls.cv.k

(Numeric) The number of (randomized) groups that the dataset is to be split into during cross validation if methodName = "CV". This value must be equal to or smaller than the number of samples.

plot

(Logical) Display the generated plots in the Plots pane in RStudio (TRUE) or not (FALSE).

export

(Logical) Export generated plots as PDF or PNG files (TRUE) or not (FALSE).

export.format

(Character, "png" or "pdf") image file format (if export = TRUE).

dpi

(Numeric) Resolution of PNG images (default is 300 dpi).

report

(Logical) Generate a report with results of this workflow (TRUE) or not (FALSE).

report.dir

(Character) Enter the name or location of the folder in which the report files are generated if report = TRUE. If NULL (the default), a new folder "Report_date-time" is created in your working directory.

export.dir

(Character) Enter the name of location of a folder in which all generated files are saved.

Author

Nicolas T. Wirth mail.nicowirth@gmail.com Technical University of Denmark License: GNU GPL (>= 2)