Make a S4/S3 object with my clinical data

Question

[Maria17]

Hello everyone,

Despite having several excel files containing my clinical data (age, tumor stage, TNM, sex, Hemolysis values), I find it difficult to analyze them separately, so I want to create an object similar to the Seurat object or any other S4, or S3 objects to access them more quickly and plot them more conveniently.

Still, I am not sure how I can do that. Due to the fact that my data is not RNA-seq data, but clinical data and qPCR data, I am unsure how to do this.

Any recommendations or solutions would be appreciated.

Thanks Maria

Answer 1

[ATpoint]

Use a SummarizedExperiment. It's assay-agnostic so you can give any assay eith features/genes/observations as rows and samples at columns. Per-column annotations (such as clinical ones) are called colData, per-row annotations (like gene type) are called rowData.

https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html

Or a SingleCellExperiment. That's a SummarizedExperiment with additional slots to store dimensionality reductions such as PCA and UMAP.