UMI4C2dds {UMI4Cats}R Documentation

UMI4Cats object to DDS object.

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.


[Package UMI4Cats version 1.0.1 Index]