rnb.execute.greedycut {RnBeads} | R Documentation

## rnb.execute.greedycut

### Description

Executes the Greedycut procedure for probe and sample filtering based on the detection p-values, and calculates statistics on its iterations.

### Usage

    rnb.execute.greedycut(
      rnb.set,
      pval.threshold = rnb.getOption("filtering.greedycut.pvalue.threshold"),
      min.coverage = rnb.getOption("filtering.coverage.threshold"),
      rc.ties = rnb.getOption("filtering.greedycut.rc.ties")
    )

### Arguments

`rnb.set` | HumanMethylation450K dataset as an object of type `RnBeadSet`.
`pval.threshold` | The P-value threshold. For further information, see the option `"filtering.greedycut.pvalue.threshold"` in `rnb.options`.
`min.coverage` | The coverage threshold. For further information, see the option `"filtering.coverage.threshold"` in `rnb.options`.
`rc.ties` | Flag indicating what the behaviour of the algorithm should be in case of ties between values of rows (probes) and columns (samples). See the corresponding parameter in `greedycut.filter.matrix` for more details.

### Value

`NULL` if `rnb.set` does not contain a matrix of detection p-values, or if all p-values denote reliable measurements. Otherwise, a list of the following elements:

"infos"

  Table summarizing the iterations of the algorithm, as returned by `greedycut.filter.matrix`.

"statistics"

  Additional statistics on all iterations, as returned by `greedycut.get.statistics`.

"iteration"

  Number of Greedycut iterations + `1` applied to the dataset, that is, a value of 1 indicates that the dataset was not modified.

"sites"

  Indices of all sites to be removed.

"samples"

  Indices of all samples to be removed.

### Author(s)

Yassen Assenov

### Examples

    library(RnBeads.hg19)
    data(small.example.object)
    greedy.result <- rnb.execute.greedycut(rnb.set.example)
    # Number of applied iterations
    greedy.result$iteration

[Package RnBeads version 2.12.2 Index]