cpgCollapse {minfi} | R Documentation

## 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

### 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.

### Value

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

If returnBlockInfo is `TRUE`:

`object` | A GenomicRatioSet of collapsed CpG clusters
`blockInfo` | A cluster annotation data frame

### Author(s)

Rafael Irizarry

### See Also

`blockFinder`

[Package minfi version 1.30.0 Index]