addGrouping: Add grouping of UMI-4C samples

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

Add grouping of UMI-4C samples

Description

This function can be used to add specific groupings to UMI4C objects.

Usage

addGrouping(
  umi4c,
  grouping = "sampleID",
  scales = 5:150,
  normalized = TRUE,
  sd = 2
)

Arguments

umi4c	UMI4C object as generated by makeUMI4C.
grouping	Name of the column in colData used to merge the samples or replicates. Set to NULL for skipping grouping. Default: "condition".
scales	Numeric vector containing the scales for calculating the domainogram.
normalized	Logical indicating whether UMI-4C profiles should be normalized to the ref_umi4c sample/group. Default: TRUE
sd	Stantard deviation for adaptative trend.

Value

Adds a new UMI4C object into the groupsUMI4C slot with samples grouped according to grouping variable.

Examples

data("ex_ciita_umi4c")

ex_ciita_umi4c <- addGrouping(ex_ciita_umi4c, grouping="condition")

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