transformCounts-methods — transformCounts,DsATAC-method • ChrAccR

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).

a new DsATAC object with normalized count data

Fabian Mueller