Description Usage Arguments Value Note Author(s) Examples
Explore the TargetExperiment and TargetExperimentList's attribute values at feature and/or gene level.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | 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)
|
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 |
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 |
see full example in TargetExperiment-class
see full example in TargetExperimentList-class
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ## 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)
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