flowWorkspace (version 3.16.0)

getSingleCellExpression,GatingSet,character-method: Return the cell events data that express in any of the single populations defined in y

Description

Returns a list of matrix containing the events that expressed in any one of the populations efined in y

Usage

"getSingleCellExpression"(x, nodes, other.markers = NULL, swap = FALSE, threshold = TRUE, ...)
"getSingleCellExpression"(x, nodes, ...)

Arguments

x

A GatingSet or GatingSetList object .

nodes

character vector specifying different cell populations

other.markers

character vector specifying the extra markers/channels to be returned besiedes the ones derived from "nodes" and "map" argument.It is only valid when threshold is set to FALSE.

swap

logical indicates whether channels and markers of flow data are swapped.

threshold

logical indicates whether to threshold the flow data by setting intensity value to zero when it is below the gate threshold.

...

other arguments

map a named list providing the mapping between node names (as specified in the gating hierarchy of the gating set) and channel names (as specified in either the desc or name columns of the parameters of the associated flowFrames in the GatingSet). see examples.

ignore.case whether to ignore case when match the marker names. Default is FALSE.

Value

A list of numerci matrices

See Also

getIndices getPopStats

Examples

## Not run: 
#   #G is a GatingSet
# 	geData(G,3)
# 	res <- getSingleCellExpression(gs[1], c("4+/TNFa+", "4+/IL2+"))
# 	res[[1]]
# 	res <- getSingleCellExpression(gs[1], c("4+/TNFa+", "4+/IL2+") , list("4+/TNFa+" = "TNFa", "4+/IL2+" = "IL2"))
# ## End(Not run)