generate_results {BEAT} | R Documentation

## Computes model methylation states for genomic region counts of a list of samples.

### Description

Computes model methylation states for genomic region counts of a list of samples.

### Usage

    generate_results(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`.

### 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)
    # compute model statistics
    generate_results(params)

[Package BEAT version 1.20.1 Index]