knownMarkersDetected: Known Markers Detected

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

Description

Known Markers Detected

Usage

knownMarkersDetected(object, ...)

## S4 method for signature 'grouped_df'
knownMarkersDetected(object, known, alpha = 0.05,
  filterPromiscuous = FALSE, promiscuousCutoff = 5L)

Arguments

object	All markers data, generated by Seurat::FindAllMarkers() return and sanitized with sanitizeMarkers().
...	Additional arguments.
known	Known markers data.frame imported by readCellTypeMarkers() or pulled from internal cellCycleMarkers data.
alpha	Alpha cutoff (adjusted P value; false discovery rate).
filterPromiscuous	Remove genes with poor specificity, that are present in as many clusters as defined by promiscuousCutoff.
promiscuousCutoff	Minimum number of clusters required to consider a gene marker promiscuous.

Value

grouped_df, grouped by "cellType" column.

Note

Both the all and known objects must contain Ensembl gene identifiers in the geneID column. We must avoid any matching operations based on the gene names, since these change often and can mismatch easily.

Author(s)

Michael Steinbaugh

See Also

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

Examples

# grouped_df ====
x <- knownMarkersDetected(
    object = all_markers_small,
    known = cellTypeMarkers[["homoSapiens"]]
)
head(x)

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