DDS object to UMI4Cats object.

Source: R/utils.R

Transforms an DDS object to a UMI4C object after applying nbinomWaldTestUMI4C.

dds2UMI4C(
  umi4c,
  dds,
  normalized = TRUE,
  padj_method = "fdr",
  padj_threshold = 0.05
)

Arguments

umi4c

UMI4C object as generated by makeUMI4C or the UMI4C constructor.
dds

DDS object as generated by nbinomWaldTestUMI4C with the DESeq2 Wald Test results
normalized

Logical indicating if the function should return normalized or raw UMI counts. Default: TRUE.
padj_method

The method to use for adjusting p-values, see p.adjust. Default: fdr.
padj_threshold

Numeric indicating the adjusted p-value threshold to use to define significant differential contacts. Default: 0.05.

Value

UMI4C object with the DESeq2 Wald Test results.