positions_to_regions {BEAT} | R Documentation

## Converts methylation counts for single genomic positions to counts for genomic regions

### Description

Converts methylation counts of a data.frame of single genomic positions into a data.frame of counts for genomic regions.

### Usage

    positions_to_regions(params, outputPath = getwd())

### Arguments

`params` | BEAT parameter object.
`outputPath` | Path to which output files will be written, the default is the current working directory.

### Format

Necessary function arguments are passed via a BEAT parameter object, which includes working path, sample names, reference sample name, model parameters and region sizes.

params

  Parameter object created by calling `makeParams`.

sample.positions.csv

  For each sample referenced by the params argument sampleNames, a corresponding csv must be present in the working directory. The csv input must contain one row per genomic position for each CG site. Columns must be chr, pos, meth, unmeth (chromosome, position, methylated counts, unmethylated counts).

### Author(s)

Kemal Akman <akmank@mpipz.mpg.de>

### See Also

See also `makeParams`.

### Examples

    # Local working directory
    localpath <- system.file('extdata', package = 'BEAT')
    # Names of samples, expected filenames are e.g. reference.positions.csv
    sampNames <- c("reference", "sample")
    # Empirical BS-conversion rates, e.g. estimated from non-CpG methylation
    convrates <- c(0.8,0.5)
    # Vector denoting reference vs. single-cell status of given samples
    is.reference <- c(TRUE,FALSE)
    params <- makeParams(localpath, sampNames, convrates, is.reference, pminus = 0.2, regionSize = 10000, minCounts = 5, verbose = TRUE, computeRegions = TRUE, computeMatrices = TRUE, writeEpicallMatrix = TRUE)
    # Pool CG positions into regions
    positions_to_regions(params)

[Package BEAT version 1.24.0 Index]