AVASet: Creating an AVASet

In R453Plus1Toolbox: A package for importing and analyzing data from Roche's Genome Sequencer System

Description

This function imports a project of Roche's Amplicon Variant Analyzer (AVA) Software. It stores all information into an extended version of the Biobase eSet.

Usage

AVASet(dirname, avaBin, file_sample, file_amp, file_reference, file_variant, file_variantHits)

Arguments

dirname	The path of the AVA project. Without AVA-CLI (AVA version < 2.6): A directory that contains the files and subdirectories "Amplicons/ProjectDef/ampliconsProject.txt", "Amplicons/Results/Variants/currentVariantDefs.txt", "Amplicons/Results/Variants", "Amplicons/Results/Align". Using AVA-CLI (recommended): Path usually ends with directory "projectfolder"
avaBin	The directory containing the AVA-CLI binary doAmplicon (usually "bin" in the AVA installation directory)
file_sample	Sample information exported with the AVA-CLI. File has to be in CSV format.
file_amp	Amplicons exported with the AVA-CLI. File has to be in CSV format.
file_reference	Reference sequences exported with the AVA-CLI. File has to be in CSV format.
file_variant	Variant information exported with the AVA-CLI. File has to be in CSV format.
file_variantHits	Report of variant hits exported with the AVA-CLI. File has to be in CSV format.

Details

The five arguments for AVA command line interface (AVA-CLI) exports are optional and useful for exported projects, when no AVA software is installed. For exporting, start the AVA-CLI with the command "doAmplicon" and use the commands "open", then "list sample", "list amplicon", "list reference", "list variant" and "report variantHits". See AVASet-class for more details.
Giving only a project directory and the path to the AVA-CLI binary doAmplicon, AVASet will import all information by accessing the AVA-CLI from within R.

An AVASet object consists of three slots to store data about
1. variants

variantForwCount/variantRevCount:

Data frames that contain the number of reads with the respective variant in forward/reverse direction.

totalForwCount/totalRevCount:

Data frames that contain the total coverage for every variant location in forward/reverse direction.

referenceSeq:

Gives the identifier of the reference sequence.

variantBase/referenceBases:

The bases changed in each variant.

start/end:

The position of the variant on the reference sequence.

canonicalPattern/name:

Short identifiers of a variant including the position and the bases changed.

2. amplicons

forwCount/revCount:

Data frames that contain the number of reads for every amplicon and each sample in forward/reverse direction.

primer1,primer2:

The primer sequences for every amplicon.

referenceSeqID:

The identifier of the reference sequence.

targetStart/targetEnd:

The coordinates of the target region.

3. reference sequences

If additional information has been loaded from Ensembl via alignShortReads, this slot knows about the chromosome, position and the strand of each reference sequence.

The structure of the variant and amplicon data is derived from the Biobase eSet and thus separated into assayData, phenoData and featureData. All information about the reference sequences is stored into an object of class AlignedRead.

The phenoData of the variants lists the sample-IDs and name, annotation and group of the read data for all samples. If available, the pico titer plate(s) (PTP) or MID(s) of each sample are shown as well (using the AVA-CLI, PTPs and MIDs cannot be importet at the moment).

Value

An instance of the AVASet class.

Note

It is recommended to use the import via AVA-CLI access. Although deprecated, the import for projects created with older version of the AVA software (< v2.6) is still possible.

Author(s)

Christoph Bartenhagen

See Also

AVASet-class, MapperSet-class, alignShortReads

Examples

# Loading a project from AVA version < 2.6:
# Load an AVA dataset containing 6 samples, 4 amplicons and 259 variants
data(avaSetExample)
avaSetExample

# Loading exported data, that was exported via AVA-CLI
# Load an AVA dataset containing 6 samples, 4 amplicons and 222 variants
# by specifying each file exported from 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")
avaSetExample

# In case AVA software is installed:
# Saying, for example, the AVA software was installed to the directory "/home/User/AVA",
# the easiest way to import a project via AVA-CLI would look like:
# avaSetExample = AVASet(dirname="myProjectDir", avaBin="/home/User/AVA/bin")

R453Plus1Toolbox documentation built on Nov. 8, 2020, 5:59 p.m.