SeuratFromDino: Create Seurat object from Dino normalized data

In JBrownBiostat/Dino: Normalization of Single-Cell mRNA Sequencing Data

Create Seurat object from Dino normalized data

Description

SeuratFromDino is a wrapper simplifying the export of Dino normalized counts to a Seurat object for secondary analysis.

Usage

SeuratFromDino(counts, doNorm = TRUE, doLog = TRUE, ...)

Arguments

counts	A numeric matrix of count data, either raw (eg. UMIs) or normalized expression.
doNorm	A logical indicating whether to normalize the input counts data before exporting results to a Seurat object. By default, it is assumed that the contents of counts raw expression which should be normalized.
doLog	A logical indicating whether normalized counts should be log transformed with a psuedocount of 1 prior to export.
...	Further arguments to pass to Dino

Value

SeuratFromDino returns a Seurat object using Dino normalized and log transformed expression (default) for downstream analysis in the Seurat pipeline.

If returnMeta = T is passed to Dino, then depth and slope results are stored in the Misc slot under the names depth and slope respectively.

Author(s)

Jared Brown

References

Brown, J., Ni, Z., Mohanty, C., Bacher, R. and Kendziorski, C. (2020). "Normalization by distributional resampling of high throughput single-cell RNA-sequencing data." bioRxiv. https://doi.org/10.1101/2020.10.28.359901

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, 495–502. https://doi.org/10.1038/nbt.3192

Examples

# raw data
data("pbmcSmall")
str(pbmcSmall)

# run Dino on raw expression matrix, output Seurat object
pbmcSmall_Seurat <- SeuratFromDino(pbmcSmall)
str(pbmcSmall_Seurat)

JBrownBiostat/Dino documentation built on June 11, 2022, 1:27 p.m.