Computes model methylation states for genomic region counts of a list of samples.
BEAT parameter object.
Path to which output files will be written, the default is the current working directory.
Necessary function arguments are passed via a BEAT parameter object, which includes working path, sample names, reference sample name, model parameters and region sizes.
Parameter object created by calling
Kemal Akman <[email protected]>
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# 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)
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