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

sce_full_Kumar

R Documentation

Kumar data sets

Description

Gene or TCC counts for scRNA-seq data set from Kumar et al. (2014), consisting of mESCs with various genetic perturbations which are cultured in different media.

Usage

sce_full_Kumar(metadata = FALSE)
sce_filteredExpr10_Kumar(metadata = FALSE)
sce_filteredHVG10_Kumar(metadata = FALSE)
sce_filteredM3Drop10_Kumar(metadata = FALSE)
sce_full_KumarTCC(metadata = FALSE)
sce_filteredExpr10_KumarTCC(metadata = FALSE)
sce_filteredHVG10_KumarTCC(metadata = FALSE)
sce_filteredM3Drop10_KumarTCC(metadata = FALSE)

Arguments

metadata

Logical, whether only metadata should be returned

Format

SingleCellExperiment

Details

This is a scRNA-seq data set originally from Kumar et al. (2014). The data set consists of gene-level read counts or TCCs (transcript compatibility counts) for mESCs from Mus musculus with various genetic perturbations which are cultured in different media. It contains 3 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_Kumar 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. Additionally, cells with a large fraction of ERCC reads were filtered out.

The sce_full_Kumar data set consists of 246 cells and 45,159 features, the sce_full_KumarTCC data set of 246 cells and 803,405 features, respectively. The filteredExpr, filteredHVG and filteredM3Drop10 are further reduced data sets. For each filtering method, we retained 10 percent of the original 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, the filteredHVG data sets were filtered on the variability of the features and only the most highly variable ones were retained (Satija et al. (2015)). 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)). For further information on the SingleCellExperiment class, see the corresponding manual. Raw data files for the original data set (GSE60749) are available from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60749.

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.

Kumar R.M., Cahan P., Shalek A.K., Satija R., DaleyKeyser A.J., Li H., Zhang J., Pardee K., Gennert D., Trombetta J.J., Ferrante T.C., Regev A., Daley G.Q., and Collins J.J. (2014) Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature 516(7529): 56–61.

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.