ovse: Example expression data.

In CaluraLab/mitology: Study of mitochondrial activity from RNA-seq data

Example expression data.

Description

This is an example dataset containing gene expression values (in normalized counts) of 40 ovarian cancer (OVC) patients extracted from the Cancer Genome Atlas (TCGA) database. This dataset should be used only with example purpose. RNA sequencing OVC data were retrieved using curatedTCGAData package. Data were then normalized with the betweenLaneNormalization function. To lighten the dataset, the consensusOVSign function was computed, which return 4 different scores, one for each OVC subtype (Chen et al, 2018, Clinical Cancer Research) and the 10 samples with the highest scores were selected for each subgroup. Further, only the mitochondrial genes included in mitology were kept. Finally, the log fold change of the IMR versus the PRO samples were computed. Further details in mitology/inst/scripts/howToGenerateOvse.Rmd.

Usage

data(ovse)

Format

An object of class SummarizedExperiment with 2388 rows and 40 columns.

CaluraLab/mitology documentation built on April 14, 2025, 8:26 a.m.