TargetExperiment-statistics: TargetExperiment and TargetExperimentList summary methods.

Description Usage Arguments Value Note Author(s) Examples

Description

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

Usage

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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

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## 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)

TarSeqQC documentation built on Nov. 8, 2020, 6:03 p.m.