sce_full_Koh: Koh data sets
In csoneson/DuoClustering2018: Data, Clustering Results and Visualization Functions From Duò et al (2018)

sce_full_Koh

R Documentation

Koh data sets

Description

Gene or TCC counts for a scRNA-seq data set from Koh et al. (2016), consisting of in vitro cultured H7 embryonic stem cells (WiCell) and H7-derived downstream early mesoderm progenitors.

Usage

sce_full_Koh(metadata = FALSE)
sce_filteredExpr10_Koh(metadata = FALSE)
sce_filteredHVG10_Koh(metadata = FALSE)
sce_filteredM3Drop10_Koh(metadata = FALSE)
sce_full_KohTCC(metadata = FALSE)
sce_filteredExpr10_KohTCC(metadata = FALSE)
sce_filteredHVG10_KohTCC(metadata = FALSE)
sce_filteredM3Drop10_KohTCC(metadata = FALSE)

Arguments

metadata

Logical, whether only metadata should be returned

Format

SingleCellExperiment

Details

This is a scRNA-seq data set originally from Koh et al. (2016). The data set consists of gene-level read counts or TCCs (transcript compatibility counts) of in vitro cultured human H7 embryonic stem cells (WiCell) and H7-derived downstream early mesoderm progenitors. It contains 9 subpopulations, defined by the cell phenotype given by the authors' annotations. The data sets have been used to evaluate the performance of clustering algorithms in Duò et al. (2018).

For the sce_full_Koh data set, all genes except those with zero counts across all cells are retained. The gene counts are gene-level length-scaled TPM values derived from Salmon (Patro et al. (2017)) quantifications (see Soneson and Robinson (2018)). For the TCC data set we estimated transcripts compatibility counts using kallisto as an alternative to the gene-level count matrix (Bray et al. (2016), Ntranos et al. (2016)).

The scater package was used to perform quality control of the data sets (McCarthy et al. (2017)). Features with zero counts across all cells, as well as all cells with total count or total number of detected features more than 3 median absolute deviations (MADs) below the median across all cells (on the log scale), were excluded.

The sce_full_Koh data set consists of 531 cells and 48,981 features, and the sce_full_KohTCC data set of 531 cells and 811,938 features. The filteredExpr, filteredHVG and filteredM3Drop10 are further reduced data sets. For each of the filtering methods, we retained 10 percent of the number of genes (with a non-zero count in at least one cell) in the original data sets.

For the filteredExpr data sets, only the genes/TCCs with the highest average expression (log-normalized count) value across all cells were retained. Using the Seurat package (Satija et al. (2015)), the filteredHVG data sets were filtered on the variability of the features and only the most highly variable ones were retained. Finally, the M3Drop package was used to model the dropout rate of the genes as a function of the mean expression level using the Michaelis-Menten equation and select variables to retain for the filteredM3Drop10 data sets (Andrews and Hemberg (2018)).

The scater package was used to normalize the count values, based on normalization factors calculated by the deconvolution method from the scran package (Lun et al. (2016)).

This data set is provided as a SingleCellExperiment object (Lun and Risso (2017)). Raw data files for the original data set (SRP073808) are available from https://www.ncbi.nlm.nih.gov/sra?term=SRP073808.

Value

Returns a SingleCellExperiment object.

References

Andrews, T.S., and Hemberg, M. (2018). Dropout-based feature selection for scRNASeq. bioRxiv doi:https://doi.org/10.1101/065094.

Bray, N.L., Pimentel, H., Melsted, P., and Pachter, L. (2016). Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34: 525–527.

Duò, A., Robinson, M.D., and Soneson, C. (2018). A systematic performance evaluation of clustering methods for single-cell RNA-seq data. F1000Res. 7:1141.

Koh, P.W., Sinha, R., Barkal, A.A., Morganti R.M., Chen, A., Weissman, I.L., Ang, L.T., Kundaje, A., and Loh, K.M. (2016). An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development. Scientific Data 3:160109.

Lun, A.T.L., Bach, K., and Marioni, J.C. (2016) Pooling across cells to normalize single-cell RNA sequencing data with many zero counts. Genome Biol. 17(1): 75.

Lun, A.T.L., and Risso, D. (2017). SingleCellExperiment: S4 Classes for Single Cell Data. R package version 1.0.0.

McCarthy, D.J., Campbell, K.R., Lun, A.T.L., and Wills, Q.F. (2017): Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. Bioinformatics 33(8): 1179-1186.

Ntranos, V., Kamath, G.M., Zhang, J.M., Pachter, L., and Tse, D.N. (2016): Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts. Genome Biol. 17:112.

Patro, R., Duggal, G., Love, M.I., Irizarry, R.A., and Kingsford, C. (2017): Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14:417-419.

Satija, R., Farrell, J.A., Gennert, D., Schier, A.F., and Regev, A. (2015). Spatial reconstruction of single-cell gene expression data. Nat. Biotechnol. 33(5): 495–502.

Soneson, C., and Robinson, M.D. (2018). Bias, robustness and scalability in single-cell differential expression analysis. Nat. Methods, 15(4): 255-261.