transform count data for an ATAC seq dataset

# S4 method for DsATAC
transformCounts(
  .object,
  method = "quantile",
  regionTypes = getRegionTypes(.object),
  ...
)

Arguments

.object

DsATAC object

method

transformation method to be applied. Currently only 'log2', 'log10', 'quantile' (quantile normalization), 'percentile' (percentile normalization),'rankPerc' (rank percentile), 'vst' (DESeq2 Variance Stabilizing Transformation), 'batchCorrect' (limma batch effect removal), tf-idf', 'CPM' (counts per million), and 'RPKM' (RPKM normalization) are supported

regionTypes

character vector specifying a name for the region type in which count data should be normalized(default: all region types)

...

other arguments depending on the method used. For 'batchCorrect' it should be arguments passed on to limma::removeBatchEffect (most importantly, the batch argument).

Value

a new DsATAC object with normalized count data

Author

Fabian Mueller