POMA EDA Example
19 May 2021
Contents
Compiled date: 2021-05-19
Last edited: 2021-04-16
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 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
