getDiffAcc-methods — getDiffAcc,DsATAC-method • ChrAccR

Compute differential accessibility

# S4 method for DsATAC
getDiffAcc(
  .object,
  regionType,
  comparisonCol,
  grp1Name = NULL,
  grp2Name = NULL,
  adjustCols = character(0),
  method = "DESeq2",
  diffObj = NULL
)

Arguments

.object: DsATAC object
regionType: character string specifying the region type
comparisonCol: column name in the sample annotation table to base the comparison on
grp1Name: name of the first group in the comparison. if not specified, it will be taken as the first factor level specified in the sample annotation table in 'comparisonCol'.
grp2Name: name of the second group (reference) in the comparison. if not specified, it will be taken as the first factor level specified in the sample annotation table in 'comparisonCol'.
adjustCols: column names in the sample annotation potentially used to create the design matrix
method: Method for determining differential accessibility. Currently only 'DESeq2' is supported
diffObj: optional differential object to avoid computing it for each comparison and thus reduce runtime

Value

a data.frame containing differential accessibility information

Author

Fabian Mueller

Examples

if (FALSE) {
dsa <- ChrAccRex::loadExample("dsAtac_ia_example")
daTab <- getDiffAcc(dsa, "IA_prog_peaks", "stimulus", grp1Name="S", grp2Name="U", adjustCols=c("cellType", "donor"))
}