register_top_value_methods {cola} | R Documentation

## Register user-defined top-value methods

### Description

Register user-defined top-value methods

### Usage

    register_top_value_methods(..., validate = TRUE)

### Arguments

`...` | A named list of functions.
`validate` | Whether validate the functions.

### Details

The user-defined function should accept one argument which is the data matrix where the scores are calculated by rows. Rows with top scores are treated as "top rows" in cola analysis. Following is how we register "SD" (standard deviation) top-value method:

      register_top_value_methods(SD = function(mat) apply(mat, 1, sd))

Of course, you can use `rowSds` to give a faster calculation of row SD:

      register_top_value_methods(SD = rowSds)

The registered top-value method will be used as defaults in `run_all_consensus_partition_methods`.

To remove a top-value method, use `remove_top_value_methods`.

There are four default top-value methods:

"SD"

  standard deviation, by `rowSds`.

"CV"

  coefficient variance, calculated as `sd/(mean+s)` where `s` is the 10^th percentile of all row means.

"MAD"

  median absolute deviation, by `rowMads`.

"ATC"

  the `ATC` method.

### Value

No value is returned.

### Author(s)

Zuguang Gu <z.gu@dkfz.de>

### See Also

`all_top_value_methods` lists all registered top-value methods.

### Examples

    all_top_value_methods()
    register_top_value_methods(
        ATC_spearman = function(mat) ATC(mat, method = "spearman")
    )
    all_top_value_methods()
    remove_top_value_methods("ATC_spearman")

[Package cola version 1.8.1 Index]