makeParams {BEAT} | R Documentation

## Creates a parameter object of arguments to be used with other BEAT functions.

### Description

Creates a parameter object of arguments to be used with other BEAT functions.

### Usage

    makeParams(localpath = getwd(), sampNames, convrates, is.reference, pminus = 0.2, regionSize = 10000, minCounts = 5, verbose = TRUE, computeRegions = TRUE, computeMatrices = TRUE, writeEpicallMatrix = TRUE)

### Arguments

`localpath` | Full path to working directory from which files are read and where results are saved.
`sampNames` | Vector of sample names to be analyzed.
`convrates` | Vector of empirically determined bisulfite conversion rates per sample. Determines p+, the model parameter for incomplete conversion (false negative rates).
`is.reference` | Vector of reference (TRUE) vs. single-cell (FALSE) status per sample.
`pminus` | Model parameter for false conversion (false positive rate).
`regionSize` | Region size in nucleotides into which genomic sites are grouped.
`minCounts` | Minimum counts necessary for each region to be included in epimutation modeling and analysis.
`verbose` | Shows more verbose console output during computation steps.
`computeRegions` | If set to TRUE, regions will be recomputed from individual positions and saved as cpgregions.RData objects for each sample.
`computeMatrices` | If set to TRUE, model parameters will be recomputed and saved as results.RData objects for each sample.
`writeEpicallMatrix` | If set to TRUE, epimutation calls will be written as RData object.

### Value

The function `makeParams` returns :

`params` | Parameter object to be used in other BEAT functions.

### Author(s)

Kemal Akman <akmank@mpipz.mpg.de>

### 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)
    # Example usage of the params object
    positions_to_regions(params)

[Package BEAT version 1.22.0 Index]