TargetExperimentList-constructor: TargetExperimentList constructor

In TarSeqQC: TARgeted SEQuencing Experiment Quality Control

Description

TargetExperimentList creates a TargetExperimentList object containing a set of targeted sequencing experiment results, all those, carried out using the same bed file. Feature parameter specifies what represent each panel element (bed file row). Attribute parameter indicates which attribute would be analyzed, 'coverage' or 'medianCounts' and should be specified in order to indicate which coverage or medianCounts should be conserved.

Usage

TargetExperimentList(TEList, feature = NULL, attribute = "coverage")

Arguments

TEList	List containing all the TargetExperiment objects corresponding to the experiments that will be compared.
feature	Character indicating the name of the feature that will be explored (e.g 'amplicon', 'transcript', 'gene').
attribute	Character indicating the name of the attribute that will be explored. Should be 'coverage' or 'medianCounts'.

Value

TargetExperimentList object.

Note

see full example in TargetExperimentList-class

Author(s)

Gabriela A. Merino [e-mail], Cristobal Fresno [e-mail], Yanina Murua [e-mail], Andrea S. Llera [e-mail] and Elmer A. Fernandez [e-mail]

See Also

TargetExperimentList-class1

Other TargetExperimentList: TargetExperimentList-class, 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)

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