dds2UMI4C: DDS object to UMI4Cats object.

In Pasquali-lab/UMI4Cats: UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

DDS object to UMI4Cats object.

Description

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

Usage

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.

Pasquali-lab/UMI4Cats documentation built on March 23, 2024, 9:42 p.m.