Learn R Programming
PREDA (version 1.18.0)

PREDAResultsGetObservedFlags: extract genomic positions with significant alterations as a matrix of flags from a PREDAResults object

Description

extract genomic positions with significant alterations as a matrix of flags from a PREDAResults object

Usage

# PREDAResultsGetObservedFlags(.Object, qval.threshold=0.05,
# smoothStatistic.tail=NULL, smoothStatistic.threshold=NULL,
# null.value=0, significant.value=1)


PREDAResultsGetObservedFlags(.Object, ...)

Arguments

.Object
An object of class PREDAResults or PREDADataAndResults
...
See below
qval.threshold:
q-value threshold used to identify significant genomic positions

smoothStatistic.tail:
Possible values are "upper" or "lower". This parameter specify if only one tail of the smoothed statististic distribution must be considered. If it is NULL, both tails are used and smoothStatistic.threshold is ignored.

smoothStatistic.threshold:
Threshold on smoothStatistic values to select significant genomic regions.

null.value:
Value (flag) assigned to not significant positions

significant.value:
Value (flag) assigned to significant positions