knownMarkersDetected: Known Markers Detected

Description Usage Arguments Value Note Author(s) See Also Examples

Description

Known Markers Detected

Usage

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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

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# 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.