dgram {UMI4Cats} | R Documentation

## 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)

[Package UMI4Cats version 1.2.1 Index]