Class VariantInfo

Description

S4 class for storing information about variants

Details

This class extends the class GRanges without adding any extra slots. The main difference is that VariantInfo objects always have a metadata column “MAF” that contains minor allele frequencies (MAFs). A special summary method allows for computing statistics about MAFs and types of variants.

Objects of this class should only be created and manipulated by the constructors and accessors described below, as only these methods ensure the integrity of the created objects. Direct modification of object slots is strongly discouraged!

Constructors

variantInfo

signature(x="missing"): creates an empty VariantInfo object

variantInfo

signature(x="GRanges"): coerces a GRanges object to class VariantInfo by adding a “MAF” metadata column that is initialized with NA values.

Furthermore, see the help page of readVariantInfo.

Accessors

MAF

signature(object="VariantInfo"): returns a numeric vector with the minor allele frequencies (MAFs).

Methods

summary

signature(object="VariantInfo"): computes and prints a summary about the MAFs and variant types (if available); this method returns a list with summarized values.

All other methods, including sub-setting, are inherited from the GRanges class.

Author(s)

Ulrich Bodenhofer bodenhofer@bioinf.jku.at

References

http://www.bioinf.jku.at/software/podkat

See Also

GRanges, readVariantInfo, genotypeMatrix, readGenotypeMatrix

Examples

vcfFile <- system.file("examples/example1.vcf.gz", package="podkat")

## read variant info directly from VCF file
vInfo <- readVariantInfo(vcfFile, omitZeroMAF=FALSE)
vInfo
summary(vInfo)

## read full genotype from VCF file
geno <- readGenotypeMatrix(vcfFile)

## display summary of variant info stored in genotype matrix
summary(variantInfo(geno))

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(podkat)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
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: 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: Biostrings
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/podkat/VariantInfo-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: VariantInfo-class
> ### Title: Class 'VariantInfo'
> ### Aliases: VariantInfo-class class:VariantInfo VariantInfo variantInfo
> ###   variantInfo,missing-method variantInfo,GRanges-method MAF
> ###   MAF,VariantInfo-method show,VariantInfo-method
> ###   summary,VariantInfo-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> vcfFile <- system.file("examples/example1.vcf.gz", package="podkat")
> 
> ## read variant info directly from VCF file
> vInfo <- readVariantInfo(vcfFile, omitZeroMAF=FALSE)
> vInfo
VariantInfo object with 3117 ranges and 2 metadata columns:
           seqnames           ranges strand |         type       MAF
              <Rle>        <IRanges>  <Rle> |     <factor> <numeric>
     snv:1     chr1       [ 79,  79]      * |   TRANSITION    0.0000
     snv:2     chr1       [281, 281]      * | TRANSVERSION    0.0000
     snv:6     chr1       [428, 428]      * | TRANSVERSION    0.1025
     snv:7     chr1       [501, 501]      * |   TRANSITION    0.0900
     snv:8     chr1       [536, 536]      * | TRANSVERSION    0.0000
       ...      ...              ...    ... .          ...       ...
  snv:3840     chr1 [199676, 199676]      * | TRANSVERSION    0.2500
  snv:3842     chr1 [199696, 199696]      * | TRANSVERSION    0.0025
  snv:3843     chr1 [199812, 199812]      * | TRANSVERSION    0.0025
  snv:3844     chr1 [199879, 199879]      * | TRANSVERSION    0.0025
  snv:3845     chr1 [199956, 199956]      * | TRANSVERSION    0.0000
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> summary(vInfo)
Variant info:
	Number of variants: 3117 

	Mean MAF:    0.01751203 
	Median MAF:  0 
	Minimum MAF: 0 
	Maximum MAF: 0.455 

	INDEL:           0 ( 0.0%)
	MULTIPLE:        0 ( 0.0%)
	TRANSITION:   1098 (35.2%)
	TRANSVERSION: 2019 (64.8%)
	UNKNOWN:         0 ( 0.0%)
> 
> ## read full genotype from VCF file
> geno <- readGenotypeMatrix(vcfFile)
> 
> ## display summary of variant info stored in genotype matrix
> summary(variantInfo(geno))
Variant info:
	Number of variants: 962 

	Mean MAF:    0.05674116 
	Median MAF:  0.0075 
	Minimum MAF: 0.0025 
	Maximum MAF: 0.455 

	no metadata column 'type' available
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>