generate_results: Computes model methylation states for genomic region counts...

In BEAT: BEAT - BS-Seq Epimutation Analysis Toolkit

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 <[e-mail]>

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)

BEAT documentation built on Nov. 8, 2020, 5:38 p.m.