Amplicon Variant Analyzer data import

Description

This is an example of an link{AVASet-class} object containing the output of Roche's Amplicon Variant Analyzer Software. It consists of 6 samples, 4 amplicons and 4 variants. The variants were previously filtered according to the amplicon coverage (see setVariantFilter for details about filtering an AVASet object).

Usage

data(avaSetFiltered)

Format

Formal class 'AVASet'

Source

‘Next-generation sequencing technology reveals a characteristic pattern of molecular mutations in 72.8 leukemia by detecting frequent alterations in TET2, CBL, RAS, and RUNX1’ (Kohlmann A et al., J Clin Oncol. 2010 Aug 20;28(24):3858-65. Epub 2010 Jul 19)

Examples

    data(avaSetFiltered)
    avaSetFiltered

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(R453Plus1Toolbox)
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/R453Plus1Toolbox/avaSetFiltered.Rd_%03d_medium.png", width=480, height=480)
> ### Name: avaSetFiltered
> ### Title: Amplicon Variant Analyzer data import
> ### Aliases: avaSetFiltered
> ### Keywords: datasets
> 
> ### ** Examples
> 
>     data(avaSetFiltered)
>     avaSetFiltered
Variants: (forward filter = 0.1)(reverse filter = 0.1)
AVASet (storageMode: list)
assayData: 4 features, 6 samples 
  element names: variantForwCount, totalForwCount, variantRevCount, totalRevCount 
protocolData: none
phenoData
  sampleNames: Sample_1 Sample_2 ... Sample_6 (6 total)
  varLabels: SampleID MID1 ... Annotation (7 total)
  varMetadata: labelDescription
featureData
  featureNames: C1338 C1323 C1163 C1206
  fvarLabels: name canonicalPattern ... referenceBases (7 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  

Amplicons: 
assayDataAmp:4 features,  6 samples
  element names:forwCountrevCount
featureDataAmp: 
An object of class 'AnnotatedDataFrame'
  rowNames: TET2_E11.04 TET2_E06 TET2_E11.03 TET2_E04
  varLabels: ampID primer1 ... targetStart (6 total)
  varMetadata: labelDescription

Reference sequences: 
class: AlignedRead
length: 4 reads; width: 339..346 cycles
chromosome: 4 4 4 4 
position: 106162417 106196936 106196674 106164659 
strand: + + + + 
alignQuality: NumericQuality 
alignData varLabels: name refSeqID gene 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>