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How to create a subset of a Seurat object?
Creates a Seurat object containing only a subset of the cells in the original object. Takes either a list of cells to use as a subset, or a parameter (for example, a gene), to subset on. SubsetData (object.)
How to change active ident in Seurat stack?
Im trying to change the active.ident to another column in metadata but this error keeps popping up! I recently upgraded to R version 4.0.2 from 3.6.1 The older version was working but the new one isn’t.
How to set do.clean = t when running subsetdata?
Try setting do.clean=T when running SubsetData, this should fix the problem. When we run SubsetData, we have (by default) not subsetted the raw.data slot as well, as this can be slow and usually unnecessary. This can in some cases cause problems downstream, but setting do.clean=T does a full subset.
How to subset by expression of any gene in list?
This is apparently a Seurat V3 vs V2 thing. I still would greatly appreciate guidance on exporting the resulting Seurat object to an R table containing only the genes of interest as columns and cells expressing any of those genes as rows, with normalized read data. Thanks! You can use the or operator | in subset.
How can I use Seurat for scrnaseq analysis?
Seurat is great for scRNAseq analysis and it provides many easy-to-use ggplot2 wrappers for visualization. However, this brings the cost of flexibility. For example, In FeaturePlot, one can specify multiple genes and also split.by to further split to multiple the conditions in the meta.data.
How to create a multi-condition featureplot in Seurat?
The idea is to generate a single UMAP plot for each sample and save them into a list and then arrange them by patchwork. Also make sure the metadata_column is a factor. # # Scale for ‘colour’ is already present. Adding another scale for ‘colour’, # # which will replace the existing scale. # # Scale for ‘colour’ is already present.