In diogo-branco/allenpvc: GEO accession data GSE71585 as a SingleCellExperiment

BiocStyle::markdown()

Introduction

The allenpvc data set is the supplementary data of GSE71585 encapsulated in a SingleCellExperiment object. It is a celular taxonomy of the primary visual cortex in adult mice based on single cell RNA-sequencing from Tasic et al. 2016 performed by the Allen Institute for Brain Science. In said study 49 transcriptomic cell types are identified.

Installation

The package can be installed using the chunk below.

BiocInstaller::biocLite("allenpvc")

Pre-processing and summary

The supplementary files were downloaded from the NCBI website. Those are csv files with count, RPKM, and TPM gene expression data for each cell. They were processed using R and were encapsulated in a SingleCellExperiment (SCE) data.

The original data had a small cell name mis-formatting that was easily corrected. Lastly, the expression for spike-in genes were available only in RPKM and counts, but not in TPM. Since this information was included in the SCE, the expression for those genes in the TPM matrix were filled with NAs.

Data format and metadata

This data set can be downloaded from the ExperimentHub.

library(allenpvc)
apvc <- allenpvc()

The gene expression data can be retrieved using the assay construct. The chunk below retrieves the count matrix, if you wish to retrieve the RPKM or the TPM matrix just replace the "counts" argument of assay with "rpkm" or "tpm".

head(assay(apvc, "counts")[, 1:5])

This data set also contains some important metadata, including cell type annotation of the samples and whether they passed the QC check performed in Tasic et al.. As well as many other useful information such as the Cre line driver and the neuron broad type.

head(colData(apvc))

Primary (cell) type of the first 20 cells.

head(apvc$primary_type, 20)

Broad type of the first 20 cells.

head(apvc$broad_type, 20)

Any metadata information can be accessed through the $ operator directly from the SCE object. But in the chunk below we are subsetting more than one column, thus, we must reference colData. The output shows the Cre line and QC check flag of some cells.

head(colData(apvc)[, c("cre_driver_1", "pass_qc_checks")])

Spike-in genes

This data set has information on the expression of spike-in genes. In the study ERCC spike-ins were used as well as the tdTomato. These genes are included in the same matrices as the endogenous genes, hence, it might be desirable to split the assay matrix.

The chunk below shows an example of splitting the count matrix. As previously mentioned, the spike-in expression for TPM is not available in the original supplementary data and, for said assay, is filled with NAs.

apvc_endo <- apvc[!isSpike(apvc),]
apvc_endo
apvc_spike <- apvc[isSpike(apvc),]
apvc_spike

sessionInfo()

sessionInfo()

References

Tasic, Bosiljka, et al. "Adult mouse cortical cell taxonomy revealed by single cell transcriptomics." Nature neuroscience 19.2 (2016): 335.

diogo-branco/allenpvc documentation built on May 5, 2019, 12:30 p.m.