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Select features and markers by their dictionary entries

Source: R/object.R
cs_features.Rd

cs_features() returns the identifiers of measurement columns whose dictionary entries match every supplied filter. Select features through this function rather than by splitting feature_id strings; the identifier layout is not part of the contract downstream code may parse.

cs_markers() returns the markers that have at least one intensity feature.

Usage

cs_features(
  x,
  kind = NULL,
  marker = NULL,
  compartment = NULL,
  statistic = NULL
)

cs_markers(x)

Arguments

x

A cellspec object.

kind, marker, compartment, statistic

Character vectors of allowed values, or NULL for no filter on that column.

Value

cs_features(): character vector of feature_id values in dictionary order (length 0 when nothing matches). cs_markers(): character vector of marker names in order of first appearance.

See also

Other object: cs_accessors, cs_bind(), cs_example(), cs_merge_tiles(), cs_new(), is_cellspec()

Examples

x <- cs_example()
cs_features(x, kind = "intensity", statistic = "mean")
#> [1] "cell:DAPI:mean"               "cell:CD3e:mean"              
#> [3] "cell:Pan-Cytokeratin:mean"    "cell:FOXP3:mean"             
#> [5] "nucleus:DAPI:mean"            "nucleus:CD3e:mean"           
#> [7] "nucleus:Pan-Cytokeratin:mean" "nucleus:FOXP3:mean"          
cs_features(x, marker = "FOXP3")
#> [1] "cell:FOXP3:mean"      "cell:FOXP3:median"    "nucleus:FOXP3:mean"  
#> [4] "nucleus:FOXP3:median"
cs_markers(x)
#> [1] "DAPI"            "CD3e"            "Pan-Cytokeratin" "FOXP3"