PomaMultivariate {POMA} | R Documentation |
PomaMultivariate() allows users to perform different multivariate statistical analysis on MS data.
PomaMultivariate( data, method = "pca", components = 5, center = FALSE, scale = FALSE, labels = FALSE, load_length = 1, ellipse = TRUE, validation = "Mfold", folds = 5, nrepeat = 10, vip = 1.5, num_features = 10 )
data |
A MSnSet object. First |
method |
A multivariate method. Options are: "pca", "plsda" and "splsda". |
components |
Numeric. Number of components to include in the model. Default is 5. |
center |
Logical that indicates whether the variables should be shifted to be zero centered. Default is FALSE. |
scale |
Logical that indicates whether the variables should be scaled to have unit variance before the analysis takes place. Default is FALSE. |
labels |
Logical indicating if sample names should be plotted or not. |
load_length |
Numeric between 1 and 2. Define the length of biplot loadings. Default is 1. |
ellipse |
Logical that indicates whether a 95%CI ellipse should be plotted in scores plot. Default is TRUE. |
validation |
(Only for "plsda" and "splsda" methods) Validation method. Options are "Mfold" and "loo". |
folds |
(Only for "plsda" and "splsda" methods) Numeric. Number of folds for Mfold validation method (default is 5). If the validation method is loo, this value will become to 1. |
nrepeat |
(Only for "plsda" and "splsda" methods) Numeric. Number of iterations for the validation method selected. |
vip |
(Only for "plsda" method) Numeric indicating VIP cutoff to select features that will be displayed in vip plot. |
num_features |
(Only for "splsda" method) Numeric. Number of variables selected to discriminate groups. |
A list with all results for multivariate statistical analysis including plots and data frames.
Pol Castellano-Escuder
data("st000336") # PCA st000336 %>% PomaImpute() %>% PomaNorm() %>% PomaOutliers() %>% PomaMultivariate(method = "pca") # PLSDA st000336 %>% PomaImpute() %>% PomaNorm() %>% PomaOutliers() %>% PomaMultivariate(method = "plsda", vip = 1) # sPLSDA st000336 %>% PomaImpute() %>% PomaNorm() %>% PomaOutliers() %>% PomaMultivariate(method = "splsda")