nbinomWaldTestUMI4C: Differential UMI4C contacts using DESeq2 Wald Test

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

Differential UMI4C contacts using DESeq2 Wald Test

Description

Takes the smooth monotone fit count values and infers the differential UMI4C contacts using DESeq2 Wald Test from DESeq2 package.

Usage

nbinomWaldTestUMI4C(dds, query_regions = NULL)

Arguments

dds	DDS object as generated by smoothMonotoneUMI4C with the smooth monotone fit counts
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.

Details

This function back-transform fitted values to the scale of raw counts and scale them across the samples to obtain normalized factors using normalizationFactors from DESeq2 package. To detect differences between conditions, the DESeq2

Value

DDS object with the DESeq2 Wald Test results, with results columns accessible with the results function.

Pasquali-lab/UMI4Cats documentation built on Nov. 3, 2024, 3:10 p.m.