inds_get_ff.RdFrom a matrix of indices generated with fcexpr::wsp_get_indices flowframes are generated. Only those events within the selected population are included in flowframes. By default no compensation will be applied on fluorescence intensites. This can be done afterwards though with in appropriate compensation matrix.
inds_get_ff(
ind_mat,
population,
alias_attr_name = "short_names",
path_attr_name = "FilePath",
downsample = 1,
inverse_transform = c(T, F),
lapply_fun = lapply,
...
)a list of indices matrices, preferentially generated with fcexpr::wsp_get_indices
which population (=node, =gate) to subset flowFrames on; must be a column name of ind_mat or an alias stored in alias_attr_name
the name of attribute containing aliases (shortest unique names) of node-names (gating paths)
the name of attribute containing the path (url) to the fcs file on which to apply the subsetting
numeric, if < 0 then a fraction of events is sampled, if > 0 an absolute number of events is sampled; or set to "min" which will lead to downsampling each flowframe to the number of events in the flowframe with lowest number of events; can be a single value to treat all FCS files equally or can be a vector of same length as FCS files
return inverse- (T) or logicle- (F) transform or both (c(T,F))
lapply function name, unquoted; lapply, pbapply::pblapply or parallel::mclapply are suggested
additional argument to the lapply function; mainly mc.cores when parallel::mclapply is chosen as lapply_fun
list of flow frames, one for each ind_mat
if (FALSE) {
ind_mat <- fcexpr::wsp_get_indices("mypath/my.wsp")
ff <- inds_get_ff(ind_mat = ind_mat, population = "CD8+")
}