cpgCollapse error
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Last seen 3 months ago
United Kingdom

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, 
                        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 !

450K blockfinder cpgCollapse minfi • 193 views

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