UMI4C-methods: UMI4C class methods

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

UMI4C class methods

Description

This page contains a summary of the different methods used to access the information contained inside the UMI4C-class object. See the details section for more information on the different accessors.

Usage

dgram(object)

dgram(object) <- value

groupsUMI4C(object, value)

groupsUMI4C(object) <- value

bait(object)

trend(object)

resultsUMI4C(object, format = "GRanges", counts = TRUE, ordered = FALSE)

## S4 method for signature 'UMI4C'
dgram(object)

## S4 replacement method for signature 'UMI4C'
dgram(object) <- value

## S4 method for signature 'UMI4C'
groupsUMI4C(object)

## S4 replacement method for signature 'UMI4C'
groupsUMI4C(object) <- value

## S4 method for signature 'UMI4C'
bait(object)

## S4 method for signature 'UMI4C'
trend(object)

## S4 method for signature 'UMI4C'
resultsUMI4C(object, format = "GRanges", counts = FALSE, ordered = FALSE)

Arguments

object	a UMI4C-class object.
value	Alternative list of dgrams to replace the current slot.
format	Either "GRanges" (default) or "data.frame", indicating the format output of the results.
counts	Logical indicating whether counts for the different region should be provided. Default: FALSE.
ordered	Logical indicating whether to sort output by significance (adjusted p-value). Default: FALSE.

Value

There are several accessors to easily retrive information from a UMI4C-class object:

• dgram: Returns a named list with the output domainograms for each sample.

• bait: Returns a GRanges object with the position of the bait.

• trend: Returns a data.frame in long format with the values of the adapative smoothen trend.

• resultsUMI4C: Returns a GRanges or data.frame with the results of the differential analysis.

See Also

UMI4C, UMI4C-class

Examples

# Access the different information inside the UMI4C object
data("ex_ciita_umi4c")
ex_ciita_umi4c <- addGrouping(ex_ciita_umi4c, grouping="condition")

dgram(ex_ciita_umi4c)
bait(ex_ciita_umi4c)
head(trend(ex_ciita_umi4c))

# Perform differential test
enh <- GRanges(c("chr16:10925006-10928900", "chr16:11102721-11103700"))
umi_dif <- fisherUMI4C(ex_ciita_umi4c, query_regions = enh, 
                       filter_low = 20, resize = 5e3)
resultsUMI4C(umi_dif)

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