Test correspondance between predicted classes and known factors

Test correspondance between predicted classes and known factors

# S4 method for HierarchicalPartition
test_to_known_factors(object, known = get_anno(object[1]),
    merge_node = merge_node_param(), verbose = FALSE)

Arguments

object

A HierarchicalPartition-class object.

merge_node

Parameters to merge sub-dendrograms, see merge_node_param.

known

A vector or a data frame with known factors. By default it is the annotation table set in hierarchical_partition.

verbose

Whether to print messages.

Value

A data frame with columns:

• number of samples

• p-values from the tests

• number of classes

The classifications are extracted for each depth.

Author

Zuguang Gu <z.gu@dkfz.de>

Examples

data(golub_cola_rh)
# golub_cola_rh already has known annotations, so test_to_known_factors()
# can be directly applied
test_to_known_factors(golub_cola_rh)
#>           ALL.AML
#> class 5.33797e-09