deseq2UMI4C: DDS object to UMI4Cats object.

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

Description

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

Usage

deseq2UMI4C(
  umi4c,
  dds,
  design = ~condition,
  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
design	A formula or matrix. The formula expresses how the counts for each fragment end depend on the variables in colData. See DESeqDataSet.
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.

UMI4Cats documentation built on Dec. 31, 2020, 2:01 a.m.