I am trying to use the cpgCollapse function in minfi to then use blockfinder
my input was:
Clusters <- cpgCollapse(GRset_SNPfilt,
what = "M",
maxGap = 500,
blockMaxGap = 2.5 * 10^5,
maxClusterWidth = 1500,
dataSummary = colMeans,
na.rm=FALSE,
returnBlockInfo = TRUE,
verbose = TRUE)
where GRset_SNPfilt is a genomic ratio set (minfi object)
but I am getting an error
[cpgCollapse] Creating annotation.
[cpgCollapseAnnotation] Clustering islands and clusters of probes.
[cpgCollapseAnnotation] Computing new annotation.
[cpgCollapseAnnotation] Defining blocks.
[cpgCollapse] Collapsing data ........ Error in GenomicRatioSet(gr = anno$anno, Beta = collapsed_meth_signal, : object 'collapsed_cn' not found
I have tried running with Beta and M values but get the same error for both
What seems to be the relevant bit of source code is as such
# Collapse data
if (verbose) message("[cpgCollapse] Collapsing data")
meth_signal <- getMethSignal(object, what = what, ...)
collapsed_meth_signal <- .cpgCollapse(
x = meth_signal,
Indexes = Indexes,
dataSummary = dataSummary,
na.rm = na.rm,
verbose = verbose)
cn <- getCN(object,...)
if (!is.null(cn)) {
collapsed_cn <- .cpgCollapse(
x = cn,
Indexes = Indexes,
dataSummary = dataSummary,
na.rm = na.rm,
verbose = verbose)
}
But I cant work out from this how I can solve my issue.
Any help is very welcome !