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minfi (version 1.18.2)

cpgCollapse: Collapse methylation values of adjacent CpGs into a summary value.

Description

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.

Usage

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,
            ...)

Arguments

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

Value

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

    If returnBlockInfo is TRUE:

  • objectA GenomicRatioSet of collapsed CpG clusters
  • blockInfoA cluster annotation data frame

Details

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.

See Also

blockFinder