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

gs_get_singlecell_expression(
  x,
  nodes,
  other.markers = NULL,
  swap = FALSE,
  threshold = TRUE,
  marginal = TRUE,
  mc.cores = getOption("mc.cores", 1L),
  inverse.transform = FALSE,
  ...
)

gs_get_singlecell_expression_by_gate(...)

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 besides 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.

marginal

logical indicates whether to the gate is treaded as 1d marginal gate. Default is TRUE, which means markers are determined either by node name or by 'map' argument explained below. When FALSE, the markers are determined by the gate dimensions. and node name and 'map' argument are ignored.

mc.cores

passed to mclapply. Default is 1, which means the process runs in serial mode. When it is larger than 1, parallel mode is enabled.

inverse.transform

logical flag indicating whether to inverse transform the data

...

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

Author

Mike Jiang wjiang2@fhcrc.org

Examples

if (FALSE) { #G is a GatingSet nodes <- c("4+/TNFa+", "4+/IL2+") res <- gs_get_singlecell_expression(gs, nodes) res[[1]] # if it fails to match the given nodes to the markers, then try to provide the mapping between node and marker explicitly res <- gs_get_singlecell_expression(gs, nodes , map = list("4+/TNFa+" = "TNFa", "4+/IL2+" = "IL2")) # It can also operate on the 2d gates by setting marginal to FALSE # The markers are no longer deduced from node names or supplied by map # Instead, it retrieves the markers that are associated with the gates nodes <- c("4+/TNFa+IFNg+", "4+/IL2+IL3+") res <- gs_get_singlecell_expression(gs, nodes, marginal = FALSE) #or simply call convenient wrapper gs_get_singlecell_expression_by_gate(gs, nodes) }