smoothMethyData {methyAnalysis} | R Documentation |
Smooth the methylation data by a sliding window with fixed width in bp unit
smoothMethyData(methyData, winSize = 250, lib = "FDb.InfiniumMethylation.hg19", p.value.detection.th = 0.05, bigMatrix=FALSE, dir.bigMatrix='.', savePrefix.bigMatrix=NULL, ...)
methyData |
A GenoSet or MethyLumiM object |
winSize |
Half sliding window size in bp unit at each side of the probe |
lib |
Methylation annotation library |
p.value.detection.th |
the threshold of detection p.value used to determine the failed probes, which will be set as NAs. |
bigMatrix |
whether to save the data as BigMatrix (designed for very large dataset) |
dir.bigMatrix |
the parent directory to save the BigMatrix data files |
savePrefix.bigMatrix |
the folder name prefix of the directory to save the BigMatrix data files. The fold name will be like this: paste(savePrefix.bigMatrix, '_bigmat', sep=”) |
... |
other parameters |
The function basically averages the probes within a local window (within winSize bp at each side of the probe).
An object with the methylation values smoothed
Pan Du
data(exampleMethyGenoSet) smoothData <- smoothMethyData(exampleMethyGenoSet)