NAMscore: NAM (iN, Ast, iMGL) Score Generator
In genejockey33000/typGumbo: Scripts and Pipelines for RNAseq Analysis
NAMscore R Documentation
NAM (iN, Ast, iMGL) Score Generator
Description
Used for assigning cells to original culture when they've been mixed
(i.e. in triple cultures or in combined monocultures). REQUIRES that
ScaleData() has been applied to ALL features (not just most variable).
NAMprep() function can be used for that purpose if necessary.
NAMscore assigns an iN, Ast, and a iMGL score value for each cell.
Input is a Seurat object and output is a Seurat object with altered metadata
that includes 4 new columns. The 3 scores (iN.score, Ast.score, and iMGL.score)
and a "NAM.bin" column that assigns each cell to predicted culture (iN, Ast, or iMGL)
or as "unk". Returned Seurat object has "NAM.bin" set as active.ident
So running DimPlot(object) will display active reduction (probably UMAP)
colored by NAM.bin
Reset active.ident to "seurat_clusters" to display cluster info on UMAP
i.e.
object <- SetIdent(object, value = "seurat_clusters")
Usage
NAMscore(object)
Arguments
object
A seurat object
Details
Note that the markers used for Neurons, Astrocytes, and Microglia are derived from
snRNAseq of independent DSEB-Astros, Ngn2 induced iNs, and Blurton-Jones protocol iMGL
all were monocultures run on separate 10x wells thus the identities were clearly known.
Genetic background for all three cultures was BR24 (XX, LPNCI, APOE(E3/E3), 90yo)
For code generating the positive markers look in "22_0628_ipsc_runs_Dropbox/SC.SN.compare.R"
Strong Positives were defined be being >= 90
genejockey33000/typGumbo documentation built on July 20, 2023, 11:45 p.m.
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| NAMscore | R Documentation |
NAM (iN, Ast, iMGL) Score Generator
Description
Used for assigning cells to original culture when they've been mixed (i.e. in triple cultures or in combined monocultures). REQUIRES that ScaleData() has been applied to ALL features (not just most variable). NAMprep() function can be used for that purpose if necessary. NAMscore assigns an iN, Ast, and a iMGL score value for each cell. Input is a Seurat object and output is a Seurat object with altered metadata that includes 4 new columns. The 3 scores (iN.score, Ast.score, and iMGL.score) and a "NAM.bin" column that assigns each cell to predicted culture (iN, Ast, or iMGL) or as "unk". Returned Seurat object has "NAM.bin" set as active.ident So running DimPlot(object) will display active reduction (probably UMAP) colored by NAM.bin Reset active.ident to "seurat_clusters" to display cluster info on UMAP i.e. object <- SetIdent(object, value = "seurat_clusters")
Usage
NAMscore(object)
Arguments
object |
A seurat object |
Details
Note that the markers used for Neurons, Astrocytes, and Microglia are derived from snRNAseq of independent DSEB-Astros, Ngn2 induced iNs, and Blurton-Jones protocol iMGL all were monocultures run on separate 10x wells thus the identities were clearly known. Genetic background for all three cultures was BR24 (XX, LPNCI, APOE(E3/E3), 90yo) For code generating the positive markers look in "22_0628_ipsc_runs_Dropbox/SC.SN.compare.R" Strong Positives were defined be being >= 90
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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