UMI4C-methods: UMI4C class methods

Description Usage Arguments Value See Also Examples

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

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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:

See Also

UMI4C, UMI4C-class

Examples

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# 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)

UMI4Cats documentation built on Dec. 31, 2020, 2:01 a.m.