gs_get_singlecell_expression {flowWorkspace} | R Documentation |
y
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(...)
x |
A |
nodes |
|
other.markers |
|
swap |
|
threshold |
|
marginal |
|
mc.cores |
passed to |
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 ignore.case whether to ignore case when match the marker names. Default is FALSE. |
A list
of numerci matrices
Mike Jiang mike@ozette.ai
gh_pop_get_indices
gs_pop_get_count_fast
## Not run: #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) ## End(Not run)