Normalizes technical biases such as sequencing depth by using a cyclic loess
to recursively normalize each pair of interaction matrices. Depends on
multiHiCcompare
.
normalizeTechnicalBiases(object, parallel = TRUE)
object | |
---|---|
parallel | Whether or not to parallelize the processing. Defaults to TRUE. |
A HiCDOCDataSet
with normalized interactions.
If parallel=TRUE
, the function
cyclic_loess
is launched in parallel mode, using bplapply
function. Before to call the function in parallel you should specify
the parallel parameters such as:
On Linux: multiParam <- BiocParallel::MulticoreParam(workers = 10)
On Windows: multiParam <- BiocParallel::SnowParam(workers = 10)
And then you can register the parameters to be used by BiocParallel:
BiocParallel::register(multiParam, default = TRUE)
filterSparseReplicates
,
filterWeakPositions
,
normalizeBiologicalBiases
,
normalizeDistanceEffect
,
HiCDOC
#>#>#>#>#>#> #> #> #>#>#>#>#>#>#>#>object <- normalizeTechnicalBiases(object)#>