Description Usage Arguments Value Author(s) Examples
Compute differential accessibility
1 2 3 4 5 6 7 8 9 10 11 | ## S4 method for signature 'DsATAC'
getDiffAcc(
.object,
regionType,
comparisonCol,
grp1Name = NULL,
grp2Name = NULL,
adjustCols = character(0),
method = "DESeq2",
diffObj = NULL
)
|
.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 |
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 |
adjustCols |
column names in the sample annotation potentially used to create the design matrix |
method |
Method for determining differential accessibility. Currently only |
diffObj |
optional differential object to avoid computing it for each comparison and thus reduce runtime |
a data.frame
containing differential accessibility information
Fabian Mueller
1 2 3 4 5 | ## Not run:
dsa <- ChrAccRex::loadExample("dsAtac_ia_example")
daTab <- getDiffAcc(dsa, "IA_prog_peaks", "stimulus", grp1Name="S", grp2Name="U", adjustCols=c("cellType", "donor"))
## End(Not run)
|
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