If this new subset is not randomly sampled, then on what criteria is it sampled? SubsetData function - RDocumentation You signed in with another tab or window. Already have an account? scanpy.pp.highly_variable_genes Scanpy 1.9.3 documentation Sign in WhichCells function - RDocumentation Seurat Methods Seurat-methods SeuratObject - GitHub Pages SubsetData : Return a subset of the Seurat object By clicking Sign up for GitHub, you agree to our terms of service and privacy statement. subset(downsample= X) Issue #3033 satijalab/seurat GitHub This approach allows then to subset nicely, with more flexibility. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 4 comments chrismahony commented on May 19, 2020 Collaborator yuhanH closed this as completed on May 22, 2020 evanbiederstedt mentioned this issue on Dec 23, 2021 Downsample from each cluster kharchenkolab/conos#115 This is pretty much what Jean-Baptiste was pointing out. Sign in Asking for help, clarification, or responding to other answers. Also, please provide a reproducible example data for testing, dput (myData). I want to subset from my original seurat object (BC3) meta.data based on orig.ident. If I have an input of 2000 cells and downsample to 500, how are te 1500 cells excluded? Eg, the name of a gene, PC1, a My analysis is helped by the fact that the larger cluster is very homogeneous - so, random sampling of ~1000 cells is still very representative. If a subsetField is provided, the string 'min' can also be . Already on GitHub? Takes either a list of cells to use as a subset, or a parameter (for example, a gene), to subset on. Downsample a seurat object, either globally or subset by a field Usage DownsampleSeurat(seuratObj, targetCells, subsetFields = NULL, seed = GetSeed()) Arguments. 5 comments williamsdrake commented on Jun 4, 2020 edited Hi Seurat Team, Error in CellsByIdentities (object = object, cells = cells) : timoast closed this as completed on Jun 5, 2020 ShellyCoder mentioned this issue Number of cells to subsample. For more information on customizing the embed code, read Embedding Snippets. Asking for help, clarification, or responding to other answers. Use MathJax to format equations. However, if you did not compute FindClusters() yet, all your cells would show the information stored in object@meta.data$orig.ident in the object@ident slot. Have a question about this project? The text was updated successfully, but these errors were encountered: This is more of a general R question than a question directly related to Seurat, but i will try to give you an idea. I would like to randomly downsample each cell type for each condition. For the new folks out there used to Satija lab vignettes, I'll just call large.obj pbmc, and downsampled.obj, pbmc.downsampled, and replace size determined by the number of columns in another object with an integer, 2999: I was trying to do the same and is used your code. I followed the example in #243, however this issue used a previous version of Seurat and the code didn't work as-is.
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