TargetExperimentList-class {TarSeqQC} | R Documentation

## TargetExperimentList S4 class implementation in R

### 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

    # 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
    }

[Package TarSeqQC version 1.12.0 Index]