waldUMI4C: DESeq2 Wald test for differential contacts

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

DESeq2 Wald test for differential contacts

Description

Using a UMI4C object, infers the differences between conditions specified in design using a Wald Test from DESeq2 package.

Usage

waldUMI4C(
  umi4c,
  query_regions = NULL,
  subset = "sum",
  design = ~condition,
  normalized = TRUE,
  padj_method = "fdr",
  padj_threshold = 0.05
)

Arguments

umi4c	UMI4C object as generated by makeUMI4C or the UMI4C constructor.
query_regions	GRanges object containing the coordinates of the genomic regions you want to use to perform the analysis in specific genomic intervals. Default: NULL.
subset	If query_regions are provided, how to subset the UMI4C object: "sum" for summing raw UMIs in fragments overlapping query_regions (default) or "overlap" for selecting overlapping fragments.
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, which can be accessed using resultsUMI4C.

Examples

data("ex_ciita_umi4c")

umi_dif <- waldUMI4C(ex_ciita_umi4c)

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