Marker Gene/Protein Identification (Deprecated)

get.markerDE() is deprecated. Use get.pbDE(.mode = "marker") instead. This function dispatches to get.pbDE with .mode = "marker".

Usage

get.markerDE(x, ...)

# S3 method for class 'TDRObj'
get.markerDE(
  x,
  .source = NULL,
  .geneset.ls = NULL,
  .id1.idx = NULL,
  .id2.idx = NULL,
  .id1 = NULL,
  .id2 = "..all.other.landmarks..",
  .id.from = "clustering",
  .model.name = "default",
  .comparison.name = NULL,
  .force.recalc = FALSE,
  .label.confidence = 0.5,
  ...
)

Arguments

x

A TDRObj, Seurat, SingleCellExperiment, or HDF5AnnData (anndataR) object processed through get.map().

...

Additional arguments passed to get.pbDE.

.source

The raw data object (or NULL for file backend).

.geneset.ls

Optional named list of character vectors for GSVA. RNA only.

.id1.idx

Optional integer vector of landmark indices for group 1.

.id2.idx

Optional integer vector of landmark indices for group 2.

.id1

Character vector of cluster/celltype IDs for group 1.

.id2

Character vector of IDs for group 2. Default "..all.other.landmarks..".

.id.from

Character: "clustering" or "celltyping".

.model.name

Character: model name (default "default").

.comparison.name

Character: comparison name, passed as .result.name.

.force.recalc

Logical: recalculate even if results exist? Default FALSE.

.label.confidence

Numeric (0-1): confidence threshold. Default 0.5.

Value

The modified x with results stored in $markerDE.

See also

get.pbDE