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 data obtained using the GPL570 platform.

study$platform_name = "GPL570"

The experimental grouping is stored into a compressed text file distributed with the package:

exp_grp_filename = system.file(
  "extdata/GSE26471", 
  "GSE26471_exp_grp.tab.gz", 
  package = "epimeddata"
)
print(exp_grp_filename)
study$exp_grp = read.table(file=gzfile(exp_grp_filename), stringsAsFactors=FALSE)

The expression data matrix is stored into a compressed text file distributed with the package:

data_filename = system.file(
  "extdata/GSE26471", 
  "GSE26471_data.tab.gz", 
  package = "epimeddata"
)
print(data_filename)
study$data = as.matrix(read.table(file=gzfile(data_filename)))

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.