summaryFeatureLev {TarSeqQC} | R Documentation

## TargetExperiment and TargetExperimentList summary methods.

### Description

Explore the TargetExperiment and TargetExperimentList's attribute values at feature and/or gene level.

### Usage

    summaryFeatureLev(object)

    ## S4 method for signature 'TargetExperiment'
    summaryFeatureLev(object)

    summaryGeneLev(object)

    ## S4 method for signature 'TargetExperiment'
    summaryGeneLev(object)

    ## S4 method for signature 'TargetExperiment'
    summary(object, ...)

    summaryIntervals(object, attributeThres = c(0, 1, 50, 200, 500, Inf),
        pool = FALSE)

    ## S4 method for signature 'TargetExperiment'
    summaryIntervals(object, attributeThres = c(0, 1,
        50, 200, 500, Inf), pool = FALSE)

    ## S4 method for signature 'TargetExperimentList'
    summary(object, ...)

    ## S4 method for signature 'TargetExperimentList'
    summaryIntervals(object,
        attributeThres = c(0, 1, 50, 200, 500, Inf), pool = FALSE)

### Arguments

`object` | TargetExperiment/TargetExperimentList class object.
`...` | required by summary.
`attributeThres` | numeric indicating the intervals extreme values required by summaryIntervals.
`pool` | logical indicating if the summary should be performed for each pool separately

### Value

according to the call one of the following objects can be returned

`data.frame` | statistics of the analyzed attribute
`data.frame` | Frequency table of the feature occurrence in the selected intervals

### Note

see full example in `TargetExperiment-class`

see full example in `TargetExperimentList-class`

### Author(s)

Gabriela A. Merino gmerino@bdmg.com.ar, Cristobal Fresno cfresno@bdmg.com.ar, Yanina Murua ymurua@leloir.org.ar, Andrea S. Llera allera@leloir.org.ar and Elmer A. Fernandez efernandez@bdmg.com.ar

### Examples

    ## Loading the TargetExperiment object
    data(ampliPanel, package="TarSeqQC")

    # Summary at feature level
    summaryFeatureLev(ampliPanel)
    # Summary at gene level
    summaryGeneLev(ampliPanel)
    # Defining the attribute interval extreme values
    attributeThres<-c(0,1,50,200,500, Inf)
    # Doing a frequency table for the attribute intervals
    summaryIntervals(ampliPanel, attributeThres=attributeThres)
    ## Loading the TargetExperimentList object
    data(TEList, package="TarSeqQC")
    # Object summary
    summary(TEList)
    # Defining the attribute interval extreme values
    attributeThres<-c(0,1,50,200,500, Inf)
    # Doing a frequency table for the attribute intervals
    summaryIntervals(TEList, attributeThres=attributeThres)

[Package TarSeqQC version 1.16.0 Index]