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 hosted on the GEO web site.

study$gse = "GSE26471"

Load data associated with this study. Data will be dowloaded from GEO to the data directory. If data is even in the data directory 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.