met.workflow | R Documentation |
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.
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"
)
mSetObj |
Enter the name of the created mSet object (see |
rowNorm |
(Character) Select the option for row-wise normalization (see |
transNorm |
(Character) Select option to transform the data (see |
scaleNorm |
(Character) Select option for scaling the data (see |
ref |
(Character) Enter the name of the reference sample or the reference feature (if |
norm.vec |
(Numeric vector) Vector with sample-specific scaling factors. Only applicable for |
class_order |
(Logical, |
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, |
nonpar |
(Logical) Use a non-parametric ANOVA test ( |
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 |
volcano.add_names |
(Logical) Display compound labels next to dots within the volcano plot ( |
volcano.label_size |
(Numerical) Enter the font size of compound labels within the volcano plot (if |
volcano.adjusted |
(Logical) Display adjusted p-values on y axis of the volcano plot ( |
pls.data |
(Character) Enter |
pls.cv.method |
(Character) Enter one of two methods for PLS-DA model (cross) validation:
|
pls.cv.k |
(Numeric) The number of (randomized) groups that the dataset is to be split into during cross validation if |
plot |
(Logical) Display the generated plots in the Plots pane in RStudio ( |
export |
(Logical) Export generated plots as PDF or PNG files ( |
export.format |
(Character, |
dpi |
(Numeric) Resolution of PNG images (default is 300 dpi). |
report |
(Logical) Generate a report with results of this workflow ( |
report.dir |
(Character) Enter the name or location of the folder in which the report files are generated if |
export.dir |
(Character) Enter the name of location of a folder in which all generated files are saved. |
Nicolas T. Wirth mail.nicowirth@gmail.com Technical University of Denmark License: GNU GPL (>= 2)
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