sanitizeMarkers: Sanitize Markers Output

In roryk/bcbioSinglecell: Single-Cell RNA-Seq Utilities

Description

Sanitize Markers Output

Usage

sanitizeMarkers(object, ...)

## S4 method for signature 'seurat'
sanitizeMarkers(object, markers)

Arguments

object	Object.
...	Additional arguments.
markers	Original Seurat::FindAllMarkers() data.frame.

Value

data.frame, arranged by adjusted P value.

Note

Seurat::FindAllMarkers() maps the counts matrix rownames correctly in the gene column, whereas Seurat::FindMarkers() maps them correctly in the rownames of the returned marker data.frame.

Author(s)

Michael Steinbaugh

See Also

Other Clustering Functions: cellTypesPerCluster, knownMarkersDetected, plotCellTypesPerCluster, plotFeatureTSNE, plotKnownMarkersDetected, plotPCElbow, plotTSNE, topMarkers

Examples

# seurat ====
object <- seurat_small

# `FindAllMarkers` return
invisible(capture.output(
    all_markers <- Seurat::FindAllMarkers(object)
))
all_sanitized <- sanitizeMarkers(
    object = object,
    markers = all_markers
)
glimpse(all_sanitized)

# `FindMarkers()` return
invisible(capture.output(
    ident_3_markers <- Seurat::FindMarkers(
        object = object,
        ident.1 = "3",
        ident.2 = NULL
    )
))
ident_3_sanitized <- sanitizeMarkers(
    object = object,
    markers = ident_3_markers
)
glimpse(ident_3_sanitized)

roryk/bcbioSinglecell documentation built on May 27, 2019, 10:44 p.m.