computeDiffAcc.rnb.nome — computeDiffAcc.rnb.nome • ChrAccR

computes differential accessibility for NOMe datasets using RnBeads functionality

computeDiffAcc.rnb.nome(
  dsn,
  cmpCols,
  regionTypes = getRegionTypes(dsn),
  covgThres = 5L,
  allPairs = TRUE,
  adjPairCols = NULL,
  adjCols = NULL,
  skipSites = FALSE,
  disk.dump = rnb.getOption("disk.dump.big.matrices"),
  disk.dump.dir = tempfile(pattern = "diffMethTables_"),
  ...
)

Arguments

dsn: DsNOMe object
cmpCols: column names of the sample annotation of the dataset that will be used for comparison
regionTypes: which region types should be processed for differential analysis.
covgThres: coverage threshold for computing the summary statistics. See RnBeads::computeDiffTab.extended.site for details.
allPairs: Logical indicating whether all pairwise comparisons should be conducted, when more than 2 groups are present
adjPairCols: argument passed on to rnb.sample.groups. See its documentation for details.
adjCols: not used yet
skipSites: flag indicating whether differential methylation in regions should be computed directly and not from sites. This leads to skipping of site-specific differential methylation
disk.dump: Flag indicating whether the resulting differential methylation object should be file backed, ie.e the matrices dumped to disk
disk.dump.dir: disk location for file backing of the resulting differential methylation object. Only meaningful if disk.dump=TRUE. must be a character specifying an NON-EXISTING valid directory.
...: arguments passed on to binary differential methylation calling. See RnBeads::computeDiffTab.extended.site for details.

Value

an RnBDiffMeth object. See class description for details.

Author

Fabian Mueller