makeParams {BEAT} | R Documentation |
Creates a parameter object of arguments to be used with other BEAT functions.
makeParams(localpath = getwd(), sampNames, convrates, is.reference, pminus = 0.2, regionSize = 10000, minCounts = 5, verbose = TRUE, computeRegions = TRUE, computeMatrices = TRUE, writeEpicallMatrix = TRUE)
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. |
The function makeParams
returns :
params |
Parameter object to be used in other BEAT functions. |
Kemal Akman <akmank@mpipz.mpg.de>
# 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)