TargetExperimentList-class: TargetExperimentList S4 class implementation in R

Description Slots Features Functions Author(s) See Also Examples

Description

This S4 class represents a collection of Targeted Sequencing Experiments in R. All these experiments are characterized by a 'bed file' containing the specification of the explored 'features', as a 'feature panel'. These features could be amplicons, exons, transcripts, among others. In general each feature is associated to one gene but a gene could be related to many features. This class allows the representation and quality control of a set of Targeted Sequencing Experiment made over the same or different subjects but using always the same bed file'.

Slots

bedFile

GRanges object that models the bed file.

panels

GRanges object containing the feature/gene panels.

attribute

character indicates which attribute, 'coverage' or 'medianCounts' will be used to the analysis.

feature

character indicates the name of the analyzed features. E.g 'amplicon', 'exon', 'transcript', 'gene'.

Features

  1. Model sets of targeted sequencing experiments in R.

  2. Evaluate the performance of the targeted sequencing technique across several experiments using coverage/read counts information.

  3. Detect in early stage sequencing or library preparation errors.

  4. Report quality control results.

Functions

TargetExperimentList S4 class includes the following functions:

initialize

constructor of TargetExperimentList to generate the feature panel starting from at least two TargetExperiment objects

getBedFile, getPanels, getAttribute, getFeature

return the respective TargetExperimentList slots

setFeature

set the respective TargetExperimentList slot

show

generic output of the object

print

generic output of the object

summary

print statistics summary for the set attribute

plot

plot a summarized view of the attribute values achieved by each feature in each sample

plotGlobalAttrExpl

plot the attribute distribution for each feature

plotAttrExpl

plot the attribute distribution in each panel

plotpoolPerformance

plot the attribute distribution in each or pool

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

See Also

Rsamtools

Other TargetExperimentList: TargetExperimentList, initialize,TargetExperimentList-method, object

Examples

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# Defining the set of TargetExperiment objects
data(ampliPanel, package="TarSeqQC")
data(ampliPanel2, package="TarSeqQC")
ampliList<-list(ampliPanel, ampliPanel2)
# Defining feature parameter
feature<-"amplicon"
# Defining attribute parameter
attribute<-"coverage"
##Calling the constructor
object<-TargetExperimentList(TEList=ampliList, attribute=attribute,
    feature=feature)
setFeature(object)<-"amplicon"
## load the example dataset
data(TEList, package="TarSeqQC")
## Early exploration
# show/print
TEList
# summary
summary(TEList)
## Controlling low counts features
# Definition of the interval extreme values
attributeThres<-c(0,1,50,200,500, Inf)
# Do a frequency table for the attribute intervals
summaryIntervals(TEList, attributeThres)
# getting low counts features at gene level
getLowCtsFeatures(TEList, level="gene", threshold=50)
# exploring panel performance along several samples
g<-plot(TEList, attributeThres=attributeThres, featureLabs =TRUE)
if(interactive()){
g
}
g<-plotGlobalAttrExpl(TEList,log=FALSE)
# x11(type="cairo")
if(interactive()){
g
}
g<-plotPoolPerformance(TEList,log=FALSE)
if(interactive()){
g
}

gamerino/TarSeqQC documentation built on Feb. 3, 2020, 9:19 p.m.