Class containing essential elements for marker gene analysis.

This generator function is designed to take the original return from a Seurat marker analysis and add corresponding gene annotations.

SeuratMarkers(object, ranges, alpha = 0.05)

Arguments

object

data.frame. Unmodified Seurat::FindMarkers() or Seurat::FindAllMarkers() return.

ranges

GRanges. Gene annotations. Names must correspond to the rownames. The function will automatically subset the ranges and arrange them alphabetically.

alpha

numeric(1). Adjusted P value ("alpha") cutoff. If left NULL, will use the cutoff defined in the object.

Value

Results are arranged by adjusted P value (padj).

Note

For Seurat::FindAllMarkers() return, rownames are correctly returned in the gene column.

See also

Examples

data(seurat) object <- seurat ranges <- rowRanges(object) ## `FindMarkers()` return. invisible(capture.output( markers <- Seurat::FindMarkers( object = object, ident.1 = "1", ident.2 = NULL ) )) x <- SeuratMarkers(object = markers, ranges = ranges)
#> `Seurat::FindMarkers` return detected.
#> alpha: 0.05 #> organism: Homo sapiens #> genomeBuild: GRCh37 #> ensemblRelease: 75 #> version: 0.3.2 #> date: 2019-05-06
## `FindAllMarkers()` return. invisible(capture.output(suppressWarnings( markers <- Seurat::FindAllMarkers(object) )))
#> Calculating cluster 0
#> Calculating cluster 1
#> Calculating cluster 2
x <- SeuratMarkersPerCluster(object = markers, ranges = ranges)
#> `Seurat::FindAllMarkers` return detected.
#> 3 clusters #> alpha: 0.05 #> organism: Homo sapiens #> genomeBuild: GRCh37 #> ensemblRelease: 75 #> version: 0.3.2 #> date: 2019-05-06