RnBeads (version 1.4.0)

rnb.execute.greedycut: 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, rc.ties = rnb.getOption("filtering.greedycut.rc.ties"))

Arguments

rnb.set

HumanMethylation450K dataset as an object of type RnBeadSet.

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.

Examples

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