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Collect marker genes from a ClustoCell object

Source: R/getDatasetMarkers.R
getDatasetMarkers.Rd

Extracts positive, negative, and/or medium markers from major clusters and sub-clusters stored in a ClustoCell object.

Usage

getDatasetMarkers(
  obj,
  clusters = TRUE,
  sub_clusters = TRUE,
  positive_markers = TRUE,
  negative_markers = FALSE,
  medium_markers = FALSE,
  thresh_mode = c("n", "rank"),
  pos_thresh = 25,
  neg_thresh = 20,
  med_thresh = 10,
  verbose = TRUE
)

Arguments

obj

An object of class ClustoCell.

clusters

Logical; whether to collect markers from major clusters.

sub_clusters

Logical; whether to collect markers from sub-clusters.

positive_markers

Logical; whether to collect positive markers.

negative_markers

Logical; whether to collect negative markers.

medium_markers

Logical; whether to collect medium markers.

thresh_mode

Character; marker selection strategy. One of:

  • "rank": include all markers with ranks up to the threshold.

  • "n": include only the top n markers (rows) in rank order..

pos_thresh

Integer; threshold for positive markers.

neg_thresh

Integer; threshold for negative markers.

med_thresh

Integer; threshold for medium markers.

verbose

Logical; whether to display progress messages.

Value

An object of class DatasetMarkers.

Details

Marker selection can be controlled using rank-based or fixed-size thresholds. Separate thresholds are applied for positive, negative, and medium markers.

See also

clustoCell, markoClust

Examples

if (FALSE) { # \dontrun{
markers <- getDatasetMarkers(cc)
} # }