R: Compute methylation data spatial correlation

computeMethylationDataSpatialCorrelation {DMRcaller}

R Documentation

Compute methylation data spatial correlation

Description

This function computes the correlation of the methylation levels as a function of the distances between the Cytosines. The function returns a vector with the correlation of methylation levels at distance equal to a vector of specified thresholds.

Usage

computeMethylationDataSpatialCorrelation(methylationData, regions = NULL,
  context = "CG", distances = NULL)

Arguments

`methylationData`	the methylation data stored as a `GRanges` object with four metadata columns (see `methylationDataList`).
`regions`	a `GRanges` object with the regions where to compute the correlation. If `NULL`, the correlation is computed genome-wide.
`context`	the context in which the correlation is computed (`"CG"`, `"CHG"` or `"CHH"`).
`distances`	a `numeric` vector specifing the different values for the distances when computing the correlation.

Value

a vector with the correlation of the methylation levels for Cytosines located at distances specified in the distances vector.

Author(s)

Nicolae Radu Zabet

Examples


# load the methylation data
data(methylationDataList)

# compute spatial correlation in CG context
distances <- c(1,5,10,15)
correlation_CG_wt <- computeMethylationDataSpatialCorrelation(methylationDataList[["WT"]], 
                 context="CG", distances=distances)

[Package DMRcaller version 1.12.7 Index]