These are example annotations for 4 variants of an AVASet (try data(avaSetFiltered) to retrieve the corresponding link{AVASet-class} object).
The annotations include affected genes, exons and codons as well as resulting amino acid changes and dbSNP identifiers (if the mutation is already known).
Usage
data(avaSetFiltered_annot)
Format
Formal class 'AnnotatedVariants'
Source
‘Next-generation sequencing technology reveals a characteristic
pattern of molecular mutations in 72.8% of chronic myelomonocytic
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_annot)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> 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_annot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: avaSetFiltered_annot
> ### Title: AVASet variant annotations
> ### Aliases: avaSetFiltered_annot
> ### Keywords: datasets
>
> ### ** Examples
>
> data(avaSetFiltered_annot)
>
>
>
>
>
> dev.off()
null device
1
>