rnb.execute.pOOBAH {RnBeads} | R Documentation |
Probe signal intensities are masked based on their out-of-band signal intensities to counter hybridization failure.
rnb.execute.pOOBAH( raw.set, anno.table = NULL, pval.thresh = 0.05, verbose = FALSE )
raw.set |
Methylation dataset as an instance of |
anno.table |
Annotation for |
pval.thresh |
Computed detection p-values above this threshold are masked. Default value is 0.05. |
verbose |
If set to true, a short information is printed on how many probes are masked by the method. |
rnb.execute.pOOBAH is used to apply the method pOOBAH (P-value with OOB probes for Array Hybridization),
which was conceived by Zhou, Triche, Laird and Shen to mask probes associated with hybridization failures.
pOOBAH has been implemented in the R-package "sesame", a dependency needed for this function (see Zhou et al, 2018 and the respective Bioconductor/github pages).
pOOBAH computes the detection p-values by constructing 2 empirical cumulative density functions (eCDFs) based
on the out-of-band signal intensities of the red and the green channel, respectively, to detect hybridization failures.
The (in-band) green and red channel signal intensities of the probes are passed to the eCDFs and the probes with a
p-value higher than the given threshold (pval.thresh
) are masked, as they are considered background.
pOOBAH is applied separately to each sample.
Hybridization failures might occur due to somatic or germline deletions.
In addition, unreliable low-intensity probes might also be masked.
Returns a modified RnBeadRawSet
, in which signal intensities are masked, if their computed p-value
was greater than pval.thresh
. Note, in datasets with several samples, signal intensities of a specific probe
might be masked in sample A, but not in sample B, as pOOBAH is applied separately to each sample.
For example: the signal intensities of probe cg24488772 might be masked in sample 1, but not in sample 12.
pOOBAH method: Wanding Zhou. Adapted by Nathan Steenbuck.
library(RnBeads.hg19) data(small.example.object) filtered <- rnb.execute.pOOBAH(rnb.set.example)