Description Usage Arguments Value Author(s)
View source: R/differential_nome.R
computes differential accessibility for NOMe datasets using RnBeads
functionality
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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_"),
...
)
|
dsn |
|
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 |
allPairs |
Logical indicating whether all pairwise comparisons should be conducted, when more than 2 groups are present |
adjPairCols |
argument passed on to |
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 |
... |
arguments passed on to binary differential methylation calling. See |
an RnBDiffMeth
object. See class description for details.
Fabian Mueller
Fabian Mueller
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