View source: R/metabolomics_computation.R
met.test_normalization | R Documentation |
met.test_normalization
runs a metabolomics analysis workflow with
several normalization/transformation/scaling combinations in parallel. The workflow
includes univariate analysis (ANOVA) and multivariate analyses (PCA and PLS-DA) and
creates a report with various performance indicators that help with deciding for
optimal data preprocessing conditions.
met.test_normalization(
mSetObj,
test_conditions = NULL,
ref = NULL,
class_order = FALSE,
alpha = 0.05,
lfc = 2,
posthoc_method = "tukey",
nonpar = FALSE,
pls.cv.method = "LOOCV",
pls.cv.k = 10,
dpi = 300,
pls.data = "all",
permut.num = 500,
vip.thresh = 1,
report = FALSE,
report.dir = NULL,
export = FALSE,
export.format = "pdf",
export.dir = "met.Test_Normalization"
)
mSetObj |
Enter the name of the created mSetObj (see |
test_conditions |
(Character vector) Enter the combinations of rowNorm, transNorm,
and scaleNorm separated by "/" to be tested in the workflow. See
|
ref |
(Character vector) Enter the name(s) of the reference sample(s) or the
reference feature(s) 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 ( |
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 |
dpi |
(Numeric) Resolution of PNG images (default is 300 dpi). |
pls.data |
(Character) Enter |
permut.num |
(Numeric) Number of permutations in PLS-DA permutation tests. |
vip.thresh |
(Numeric) Enter a chosen relevance threshold for PLS-DA VIP scores. |
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 |
(Logical) Export generated plots as PDF or PNG files ( |
export.format |
(Character, |
export.dir |
(Character) Enter the name or 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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