transformCounts-DsATAC-method: transformCounts-methods

In GreenleafLab/ChrAccR: Analyzing chromatin accessibility data in R

transformCounts-methods

Description

transform count data for an ATAC seq dataset

Usage

## S4 method for signature '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(s)

Fabian Mueller

GreenleafLab/ChrAccR documentation built on March 22, 2023, 11:42 p.m.