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 a SummarizedExperiment 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

10 April 2022

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