cpgCollapse: Collapse methylation values of adjacent CpGs into a summary...
In minfi: Analyze Illumina Infinium DNA methylation arrays

Description Usage Arguments Details Value Author(s) See Also

This function groups adjacent loci into clusters with a specified maximum gap between CpGs in the cluster, and a specified maximum cluster width. The loci within each cluster are summarized resulting in a single methylation estimate per cluster.

cpgCollapse(object, what = c("Beta", "M"), maxGap = 500,
            blockMaxGap = 2.5 * 10^5, maxClusterWidth = 1500,
            dataSummary = colMeans, na.rm = FALSE,
            returnBlockInfo = TRUE, islandAnno = NULL, verbose = TRUE,
            ...)

`object`	An object of class `[Genomic]MethylSet` or `[Genomic]RatioSet`.
`what`	Should operation be performed on the M-scale or Beta-scale?
`maxGap`	Maximum gap between CpGs in a cluster
`blockMaxGap`	Maximum block gap
`maxClusterWidth`	Maximum cluster width
`dataSummary`	Function used to summarize methylation across CpGs in the cluster.
`na.rm`	Should NAs be removed when summarizing? Passed on to the dataSummary function.
`returnBlockInfo`	Should the block annotation table be returned in addition to the block table?
`islandAnno`	Which Island annotation should be used. `NULL` indicates the default. This argument is only useful if the annotatio object contains more than one island annotation.
`verbose`	Should the function be verbose?
`...`	Passed on to getMethSignal and getCN. Can be used to specify

This function is used as the first step of block-finding. It groups adjacent loci into clusters with a default maximum gap of 500bp and a maximum cluster width of 1,500bp. The loci within each cluster are then summarized (using the mean by default) resulting in a single methylation estimate per cluster. Cluster estimates from open-sea probes are used in block-finding.

If returnBlockInfo is FALSE: a GenomicRatioSet of collapsed CpG clusters.

If returnBlockInfo is TRUE: