| Title: | Data for the spqn package |
|---|---|
| Description: | Bulk RNA-seq from GTEx on 4,000 randomly selected, expressed genes. Data has been processed for co-expression analysis. |
| Authors: | Yi Wang [cre, aut], Kasper Daniel Hansen [aut] |
| Maintainer: | Yi Wang <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.25.0 |
| Built: | 2026-10-10 10:40:21 UTC |
| Source: | https://github.com/bioc/spqnData |
A random sample of 4,000 expressed genes (protein-coding or lincRNAs) from GTEx v6p. The tissue is Adipose Subcutaneous.
data("gtex.4k")data("gtex.4k")
An object of class SummarizedExperiment.
Data is 350 samples from GTEx v6p. The tissue is Adipose Subcutanous.
We first selected protein-coding or lincRNAs based on the supplied annotation
files. Next we kept genes with a median log2(RPKM) expression greater
than zero. This resulted in a data matrix with 12,267 genes of which
11,911 are protein-coding. We stored the mean expression value per gene
in rowData(gtex.4k)$ave_logrpkm.
We next mean centered and variance scaled the expression values so all
genes have zero mean and variance 1. We then removed 4 principal
components from this data matrix using the
removePrincipalComponents function from the WGCNA package.
Finally, we randomly selected 4,000 genes.
Additional information on the genes are present in the
rowData. The type of gene (lincRNA or protein-coding) is present
in the gene_type column. The average expression of each gene on
the log2(RPKM)-scale, prior to removing principal components, are
present in the ave_logrpkm column.
Original data from gtexportal.org. A script for downloading and
processing the paper is included in scripts/gtex.Rmd.
data(gtex.4k)data(gtex.4k)