cpgCollapse error
0
0
Entering edit mode
@5e9d7ee1
Last seen 7 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, 
                        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 !

450K blockfinder cpgCollapse minfi • 572 views
ADD COMMENT

Login before adding your answer.

Traffic: 935 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6