In fchuffar/epimedtools: Useful Tools Allowing Multi-Omics Analysis

knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

Loading the epimedtools library

library(epimedtools)

Creating a new study.

study = create_study()

This study deals with the GEO accession GSE26471, its series_matrix is distributed with the package

series_matrix_filename = system.file(
  "extdata/GSE26471", 
  "GSE26471_series_matrix.txt.gz", 
  package = "epimeddata"
)
print(series_matrix_filename)
study$series_matrix_filename = series_matrix_filename

Load data associated with this study. Data is even on the hard drive, it is directly load from there.

study$get_gset()

Extract data matrix.

dim(study$get_data())

Extract experimental grouping dataframe.

dim(study$get_exp_grp())

Plot density of expression for this 1-sample dataset.

plot(density(study$get_data()[,1]))

Saving the study on the file system.

```r study$save("/tmp/study.rds") ````

fchuffar/epimedtools documentation built on Feb. 3, 2024, 2:21 a.m.