1 Installation

Run the following code to install the Bioconductor version of package.

# install.packages("BiocManager")
BiocManager::install("POMA")

2 Load POMA

library(POMA)

3 Automatic EDA Report

The following function will return an Exploratory Data Analysis (EDA) PDF report. The input object must be an MSnSet object.

data("st000336")
PomaEDA(st000336)

Generated EDA PDF report starts here.

4 Know your data

Your data have 57 samples, 31 features and 2 groups, that are ‘Controls’, ‘DMD’. Furthermore, 1 covariates have been found in your data. These covariates are ‘steroids’.
A 3.45% of values in your data are NAs (missing values). Variables that have NA values are ‘aspartic_acid (5)’, ‘citrulline (28)’, ‘glutamic_acid (15)’, ‘methionine (3)’, ‘x3_hba (1)’, ‘a_kg (1)’, ‘citrate (2)’, ‘fumarate (1)’, ‘lactate (2)’, ‘malate (1)’, ‘pyruvate (1)’, ‘succinate (1)’.
A 0% of values in your data are zeros.
Removed from the exploratory data analysis 0 features that only have zeros.
Removed from the exploratory data analysis 0 features that have zero variance.

4.1 Summary Table

Samples	Features	Covariates
57	31	1

Counts_Zero	Percent_Zero
0	0 %

Counts_NA	Percent_NA
61	3.45 %

4.2 Samples by Group

5 Normalization Plots

6 Group Distribution Plots

7 Outlier Detection

7 possible outliers detected in your data. These outliers are ‘DMD119.2.U02’, ‘DMD084.11.U02’, ‘DMD087.12.U02’, ‘DMD023.10.U02’, ‘DMD046.11.U02’, ‘DMD133.9.U02’, ‘DMD135.10.U02’.

sample	group	distance_to_centroid	limit_distance
DMD119.2.U02	Controls	2.742576	2.290945
DMD084.11.U02	DMD	4.522825	4.040548
DMD087.12.U02	DMD	4.252170	4.040548
DMD023.10.U02	DMD	5.653399	4.040548
DMD046.11.U02	DMD	5.580959	4.040548
DMD133.9.U02	DMD	5.349670	4.040548
DMD135.10.U02	DMD	4.055233	4.040548

8 High Correlated Features (r > 0.97)

There are 0 high correlated feature pairs in your data.

9 Heatmap and Clustering

10 Principal Component Analysis

POMA EDA Example

27 October 2020

Contents