rnb.execute.greedycut {RnBeads} | R Documentation |
Executes the Greedycut procedure for probe and sample filtering based on the detection p-values, and calculates statistics on its iterations.
rnb.execute.greedycut( rnb.set, pval.threshold = rnb.getOption("filtering.greedycut.pvalue.threshold"), min.coverage = rnb.getOption("filtering.min.coverage"), rc.ties = rnb.getOption("filtering.greedycut.rc.ties") )
rnb.set |
HumanMethylation450K dataset as an object of type |
pval.threshold |
The P-value threshold. For further information, see the option |
min.coverage |
The coverage threshold. For further information, see the option |
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
|
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:
Table summarizing the iterations of the algorithm, as returned by
greedycut.filter.matrix
.
Additional statistics on all iterations, as returned by
greedycut.get.statistics
.
Number of Greedycut iterations + 1
applied to the dataset, that is,
a value of 1 indicates that the dataset was not modified.
Indices of all sites to be removed.
Indices of all samples to be removed.
Yassen Assenov
library(RnBeads.hg19) data(small.example.object) greedy.result <- rnb.execute.greedycut(rnb.set.example) # Number of applied iterations greedy.result$iteration