UMI4C2dds: UMI4Cats object to DDS object.

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

Description

Transforms an UMI4C object to a DDS object

Usage

UMI4C2dds(umi4c, design = ~condition, query_regions = NULL, ...)

Arguments

umi4c	UMI4C object as generated by makeUMI4C or the UMI4C constructor.
design	A formula or matrix. The formula expresses how the counts for each fragment end depend on the variables in colData. See DESeqDataSet.
query_regions	GRanges object or data.frame containing the coordinates of the genomic regions you want to use to perform the analysis in specific genomic intervals. Default: NULL.
...	Other arguments to be passed to DESeq function.

Value

DDS object.

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