POMA EDA Example
26 April 2022
Contents
Compiled date: 2022-04-26
Last edited: 2021-12-12
License: GPL-3
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
