cpgCollapse | R Documentation |
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 |
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. |
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
:
object |
A GenomicRatioSet of collapsed CpG clusters |
blockInfo |
A cluster annotation data frame |
Rafael Irizarry
blockFinder
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