- 1 The
*ropls*package - 2 Context
- 3 The
*sacurine*metabolomics dataset - 4 Hands-on
- 5 Other datasets
- 6 Session info
- 7 References

The ropls R
package implements the **PCA**, **PLS(-DA)** and **OPLS(-DA)** approaches with
the original, **NIPALS**-based, versions of the algorithms
(**???**). It includes the **R2** and **Q2** quality metrics
(**???**), the permutation **diagnostics**
(**???**), the computation of the **VIP** values (**???**), the score
and orthogonal distances to detect **outliers** (**???**), as well as many
**graphics** (scores, loadings, predictions, diagnostics, outliers, etc).

The functionalities from
ropls can also
be accessed via a graphical user interface in the **Multivariate** module from
the Workflow4Metabolomics.org online
resource for computational metabolomics, which provides a user-friendly,
**Galaxy**-based environment for data pre-processing, statistical analysis, and
annotation (**???**).

**Partial Least-Squares (PLS)**, which is a latent variable regression method
based on covariance between the predictors and the response, has been shown to
efficiently handle datasets with multi-collinear predictors, as in the case of
spectrometry measurements (**???**). More recently, (**???**) introduced the
**Orthogonal Partial Least-Squares (OPLS)** algorithm to model separately the
variations of the predictors correlated and orthogonal to the response.

OPLS has a similar predictive capacity compared to PLS and improves the
**interpretation** of the predictive components and of the systematic variation
(**???**). In particular, OPLS modeling of single responses only requires
one predictive component.

**Diagnostics** such as the **Q2Y** metrics and permutation testing are of high
importance to **avoid overfitting** and assess the statistical significance of
the model. The **Variable Importance in Projection (VIP)**, which reflects both
the loading weights for each component and the variability of the response
explained by this component (**???**; **???**), can be used for
feature selection (**???**; **???**).

OPLS is available in the **SIMCA-P** commercial software (Umetrics, Umea,
Sweden; (**???**)). In addition, the kernel-based version of OPLS
(**???**) is available in the open-source R statistical environment
(**???**), and a single implementation of the linear algorithm in R has
been described recently (**???**).

The objective was to study the influence of **age**, **body mass index (bmi)**,
and **gender** on metabolite concentrations in **urine**, by analysing 183
samples from a **cohort** of adults with liquid chromatography coupled to
high-resolution mass spectrometry (**LC-HRMS**; (**???**)).

Urine samples were analyzed by using an LTQ Orbitrap in the negative ionization
mode. A total of **109 metabolites** were identified or annotated at the MSI level 1
or 2. After retention time alignment with XCMS, peaks were integrated with Quan
Browser. Signal drift and batch effect were corrected, and each urine profile
was normalized to the osmolality of the sample. Finally, the data were log10
transformed (**???**).

The volunteersâ€™ **age**, **body mass index (bmi)**, and **gender** were recorded.

We first load the ropls package:

`library(ropls)`

We then load the **sacurine** dataset which contains:

The

**dataMatrix**matrix of numeric type containing the intensity profiles (log10 transformed),The

**sampleMetadata**data frame containg sample metadata,The

**variableMetadata**data frame containg variable metadata

```
data(sacurine)
names(sacurine)
```

`## [1] "dataMatrix" "sampleMetadata" "variableMetadata"`

We attach **sacurine** to the search path and display a summary of the content
of the **dataMatrix**, **sampleMetadata** and **variableMetadata** with the
`view`

method from the
ropls package:

`attach(sacurine)`

`view(dataMatrix)`

```
## dim class mode typeof size NAs min mean median max
## 183 x 109 matrix numeric double 0.2 Mb 0 -0.3 4.2 4.3 6
## (2-methoxyethoxy)propanoic acid isomer (gamma)Glu-Leu/Ile ...
## HU_011 3.019766011 3.888479324 ...
## HU_014 3.81433889 4.277148905 ...
## ... ... ... ...
## HU_208 3.748127215 4.523763202 ...
## HU_209 4.208859398 4.675880567 ...
## Valerylglycine isomer 2 Xanthosine
## HU_011 3.889078716 4.075879575
## HU_014 4.181765852 4.195761901
## ... ... ...
## HU_208 4.634338821 4.487781609
## HU_209 4.47194762 4.222953354
```

`view(sampleMetadata)`

```
## age bmi gender
## numeric numeric factor
## nRow nCol size NAs
## 183 3 0 Mb 0
## age bmi gender
## HU_011 29 19.75 M
## HU_014 59 22.64 F
## ... ... ... ...
## HU_208 27 18.61 F
## HU_209 17.5 21.48 F
```

`## 1 data.frame 'factor' column(s) converted to 'numeric' for plotting.`

`view(variableMetadata)`

```
## msiLevel hmdb chemicalClass
## numeric character character
## nRow nCol size NAs
## 109 3 0 Mb 0
## msiLevel hmdb chemicalClass
## (2-methoxyethoxy)propanoic acid isomer 2 Organi
## (gamma)Glu-Leu/Ile 2 AA-pep
## ... ... ... ...
## Valerylglycine isomer 2 2 AA-pep:AcyGly
## Xanthosine 1 HMDB00299 Nucleo
```

`## 2 data.frame 'character' column(s) converted to 'numeric' for plotting.`

Note:

the

`view`

method applied to a numeric matrix also generates a graphical displaythe

`view`

method can also be applied to an ExpressionSet object (see below)

We perform a **PCA **on the **dataMatrix** matrix (samples as rows, variables as
columns), with the `opls`

method:

`sacurine.pca <- opls(dataMatrix)`

A **summary** of the model (8 components were selected) is printed:

```
## PCA
## 183 samples x 109 variables
## standard scaling of predictors
## R2X(cum) pre ort
## Total 0.501 8 0
```

In addition the default **summary** figure is displayed:

**Figure 1: PCA summary plot.** **Top left** `overview`

: the **scree** plot (i.e.,
inertia barplot) suggests that 3 components may be sufficient to capture most of
the inertia; **Top right** `outlier`

: this graphics shows the distances within
and orthogonal to the projection plane (**???**): the name of the samples
with a high value for at least one of the distances are indicated; **Bottom
left** `x-score`

: the variance along each axis equals the variance captured by
each component: it therefore depends on the total variance of the dataMatrix *X*
and of the percentage of this variance captured by the component (indicated in
the labels); it decreases when going from one component to a component with
higher indice; **Bottom right** `x-loading`

: the 3 variables with most extreme
values (positive and negative) for each loading are black colored and labeled.

Note:

Since

**dataMatrix**does not contain missing value, the singular value decomposition was used by default; NIPALS can be selected with the`algoC`

argument specifying the*algo*rithm (*C*haracter),The

`predI = NA`

default number of*pred*ictive components (*I*nteger) for PCA means that components (up to 10) will be computed until the cumulative variance exceeds 50%. If the 50% have not been reached at the 10th component, a warning message will be issued (you can still compute the following components by specifying the`predI`

value).

Let us see if we notice any partition according to gender, by labeling/coloring
the samples according to *gender* (`parAsColFcVn`

) and drawing the Mahalanobis
ellipses for the male and female subgroups (`parEllipseL`

).

```
genderFc <- sampleMetadata[, "gender"]
plot(sacurine.pca,
typeVc = "x-score",
parAsColFcVn = genderFc)
```