Class to contain Amplicon Variant Analyzer Output

Description

Container to store data imported from a project of Roche's Amplicon Variant Analyzer Software. It stores all information into an extended version of the Biobase ExpressionSet.

Objects from the Class

Objects can be created by calls of the form AVASet(dirname, avaBin). dirname is a character giving the proejct directory and avaBin is a character giving the path to the AVA software installation (i.e. the directory containing the doAmplicon binary). The constructor will start the AVA software command line and import all necessary data.

If the AVA software is not installed on the same machine that runs R, all data must be exported manually using the AVA Command Line Interface (AVA-CLI). After having exported all text files, the constructor AVASet(dirname, avaBin, file_sample, file_amp, file_reference, file_variant, file_variantHits) can be used to import them. See the example below.

Finally, old project folders generated by AVA software < 2.6 can be imported using AVASet(dirname). Where dirname is the path to the project folder (i.e. a directory that contains the files and subdirectories "Amplicons/ProjectDef/ampliconsProject.txt", "Amplicons/Results/Variants/currentVariantDefs.txt", "Amplicons/Results/Variants", "Amplicons/Results/Align").

Slots

assayData:

Object of class AssayData. Contains the number of reads and the total read depth for every variant and each sample in forward and reverse direction. Its column number equals nrow(phenoData).

featureData:

Object of class AnnotatedDataFrame. Contains information about the type, position and reference of each variant.

phenoData:

Object of class AnnotatedDataFrame. Contains the sample-IDs and name, annotation and group of the read data for all samples. If available, the lane, pico titer plate(s) (PTP) or MID(s) of each sample are shown as well.

assayDataAmp:

Object of class AssayData. Contains the number of reads for every amplicon and each sample in forward/reverse direction. Its column number equals nrow(featureDataAmp).

featureDataAmp:

Object of class AnnotatedDataFrame. Contains the primer sequences, reference sequences and the coordinates of the target regions for every amplicon.

referenceSequences:

Object of class AlignedRead. If additional alignment information were computed via alignShortReads, this slot knows about the chromosome, position and the strand of each reference sequence.

variantFilterPerc:

Object of class numeric. Contains a threshold to display only those variants, whose coverage (in percent) in forward and reverse direction in at least one sample is higher than this filter value. See setVariantFilter for details about setting this value.

variantFilter:

Object of class character. Contains a vector of variant names whose coverage (in percent) in forward and reverse direction in at least one sample is higher than the filter value in variantFilterPerc.

dirs:

Object of class character. Based on a directory given at instantiation of the object, it contains a vector of several directories containing all relevant AVA-project files.

experimentData:

Object of class MIAME. Contains details of the experiment.

annotation:

Object of class character. Label associated with the annotation package used in the experiment.

protocolData:

Object of class annotatedDataFrame. Contains additional information about the samples.

.__classVersion__:

Object of class Versions. Remembers the R and R453Toolbox version numbers used to created the AVASet instance.

Extends

Class eSet, directly. Class VersionedBiobase, by class "eSet", distance 2. Class Versioned, by class "eSet", distance 3.

Methods

object[i,j]:

Allows subsetting an AVASet object by features (i) and samples (j).

assayDataAmp(object), assayDataAmp(object)<-value:

Similar to assayData of the Biobase ExpressionSet, this function returns/replaces the amplicon assay data.

fDataAmp(object):

Similar to fData of the Biobase ExpressionSet, this function returns the amplicon feature data as a data frame.

featureDataAmp(object), featureDataAmp(object)<-value:

Similar to featureData of the Biobase ExpressionSet, this function returns/replaces the amplicon feature data and feature meta.

referenceSequences(object), referenceSequences(object)<-value:

Returns/replaces the reference sequence slot.

alignShortReads(object, bsGenome):

Retrieve the chromosomal positions of the amplicon sequences.

setVariantFilter(object):

Sets the filter to display only those variants, whose coverage (in percent) in forward and reverse direction in at least one sample is higher than the given value.

getVariantPercentages(object)

Computes the coverage for every variant over all reads (forward and/or reverse) and for each sample.

annotateVariants(object):

Annotates given genomic variants. See annotateVariants for details.

htmlReport(object):

Exports all (filtered) variant data into a html report. See htmlReport for details

Author(s)

Christoph Bartenhagen

See Also

MapperSet-class, annotateVariants, alignShortReads, htmlReport, setVariantFilter, getVariantPercentages

Examples

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    # sum up class structure
    showClass("AVASet")

    # load an AVA dataset containing 6 samples, 4 amplicons and 259 variants
    data(avaSetExample)
    avaSetExample

    # show contents of assay, feature and pheno data
    head(assayData(avaSetExample)$variantForwCount)
    head(assayData(avaSetExample)$totalForwCount)
    head(assayData(avaSetExample)$variantRevCount)
    head(assayData(avaSetExample)$totalRevCount)
    head(fData(avaSetExample))
    pData(avaSetExample)
    assayDataAmp(avaSetExample)
    fDataAmp(avaSetExample)
    referenceSequences(avaSetExample)

    # Use these commands to export a project from within the AVA-CLI (doAmplicon):
    # > list sample -outputFile sample.csv
    # > list amplicon -outputFile amp.csv
    # > list reference -outputFile reference.csv
    # > list variant -outputFile variant.csv
    # > report variantHits -outputFile variantHits.csv

    # Load an AVA dataset containing 6 samples, 4 amplicons and 222 variants
    # by specifying five files, that were exported with the AVA-CLI:
    projectDir = system.file("extdata", "AVASet_doAmplicon", package="R453Plus1Toolbox")
    avaSetExample = AVASet(dirname=projectDir, file_sample="sample.csv", file_amp="amp.csv", file_reference="reference.csv", file_variant="variant.csv", file_variantHits="variantHits.csv")

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