Last data update: 2014.03.03

 R: Parameters for scanning VCF files
ScanVcfParam-classR Documentation

Parameters for scanning VCF files

Description

Use ScanVcfParam() to create a parameter object influencing which records and fields are imported from a VCF file. Record parsing is based on genomic coordinates and requires a Tabix index file. Individual VCF elements can be specified in the ‘fixed’, ‘info’, ‘geno’ and ‘samples’ arguments.

Usage

  ScanVcfParam(fixed=character(), info=character(), geno=character(), 
               samples=character(), trimEmpty=TRUE, which, ...)

  ## Getters and Setters 
 
  vcfFixed(object)
  vcfFixed(object) <- value
  vcfInfo(object)
  vcfInfo(object) <- value
  vcfGeno(object)
  vcfGeno(object) <- value
  vcfSamples(object)
  vcfSamples(object) <- value
  vcfTrimEmpty(object)
  vcfTrimEmpty(object) <- value
  vcfWhich(object)
  vcfWhich(object) <- value

Arguments

fixed

A character() vector of fixed fields to be returned. Possible values are ALT, QUAL and FILTER. The CHROM, POS, ID and REF fields are needed to create the GRanges of variant locations. Because these are essential fields there is no option to request or omit them. If not specified, all fields are returned; if fixed=NA only REF is returned.

info

A character() vector naming the ‘INFO’ fields to return. scanVcfHeader() returns a vector of available fields. If not specified, all fields are returned; if info=NA no fields are returned.

geno

A character() vector naming the ‘GENO’ fields to return. scanVcfHeader() returns a vector of available fields. If not specified, all fields are returned; if geno=NA no fields are returned and requests for specific samples are ignored.

samples

A character() vector of sample names to return. samples(scanVcfHeader()) returns all possible names. If not specified, data for all samples are returned; if either samples=NA or geno=NA no fields are returned. Requests for specific samples when geno=NA are ignored.

trimEmpty

A logical(1) indicating whether ‘GENO’ fields with no values should be returned.

which

A GRanges describing the sequences and ranges to be queried. Variants whose POS lies in the interval(s) [start, end] are returned. If which is not specified all ranges are returned.

object

An instance of class ScanVcfParam.

value

An instance of the corresponding slot, to be assigned to object.

...

Arguments passed to methods.

Objects from the Class

Objects can be created by calls of the form ScanVcfParam().

Slots

which:

Object of class "RangesList" indicating which reference sequence and coordinate variants must overlap.

fixed:

Object of class "character" indicating fixed fields to be returned.

info:

Object of class "character" indicating portions of ‘INFO’ to be returned.

geno:

Object of class "character" indicating portions of ‘GENO’ to be returned.

samples:

Object of class "character" indicating the samples to be returned.

trimEmpty:

Object of class "logical" indicating whether empty ‘GENO’ fields are to be returned.

Functions and methods

See 'Usage' for details on invocation.

Constructor:

ScanVcfParam:

Returns a ScanVcfParam object. The which argument to the constructor can be one of several types, as documented above.

Accessors:

vcfFixed, vcfInfo, vcfGeno, vcfSamples, vcfTrimEmpty, vcfWhich:

Return the corresponding field from object.

Methods:

show

Compactly display the object.

Author(s)

Martin Morgan and Valerie Obenchain

See Also

readVcf

Examples

  ScanVcfParam()

  fl <- system.file("extdata", "structural.vcf", package="VariantAnnotation")
  compressVcf <- bgzip(fl, tempfile())
  idx <- indexTabix(compressVcf, "vcf")
  tab <- TabixFile(compressVcf, idx)
  ## ---------------------------------------------------------------------
  ## 'which' argument
  ## ---------------------------------------------------------------------
  ## To subset on genomic coordinates, supply an object 
  ## containing the ranges of interest. These ranges can
  ## be given directly to the 'param' argument or wrapped
  ## inside ScanVcfParam() as the 'which' argument. 

  ## When using a list, the outer list names must correspond to valid
  ## chromosome names in the vcf file. In this example they are "1" 
  ## and "2".
  gr1 <- GRanges("1", IRanges(13219, 2827695, name="regionA"))
  gr2 <- GRanges(rep("2", 2), IRanges(c(321680, 14477080), 
                 c(321689, 14477090), name=c("regionB", "regionC")))
  grl <- GRangesList("1"=gr1, "2"=gr2)
  vcf <- readVcf(tab, "hg19", grl)

  ## Names of the ranges are in the 'paramRangeID' metadata column of the
  ## GRanges object returned by the rowRanges() accessor.
  rowRanges(vcf)

  ## which can be used for subsetting the VCF object
  vcf[rowRanges(vcf)$paramRangeID == "regionA"]
 
  ## When using ranges, the seqnames must correspond to valid
  ## chromosome names in the vcf file.
  gr <- unlist(grl, use.names=FALSE)
  vcf <- readVcf(tab, "hg19", gr)
 
  ## ---------------------------------------------------------------------
  ## 'fixed', 'info', 'geno' and 'samples' arguments
  ## ---------------------------------------------------------------------
  ## This param specifies the "GT" 'geno' field for a single sample
  ## and the subset of ranges in 'which'. All 'fixed' and 'info' fields 
  ## will be returned. 
  ScanVcfParam(geno="GT", samples="NA00002", which=gr)
 
  ## Here two 'fixed' and one 'geno' field are specified
  ScanVcfParam(fixed=c("ALT", "QUAL"), geno="GT", info=NA) 

  ## Return only the 'fixed' fields
  ScanVcfParam(geno=NA, info=NA)

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)

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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(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/VariantAnnotation/ScanVcfParam-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ScanVcfParam-class
> ### Title: Parameters for scanning VCF files
> ### Aliases: ScanVcfParam ScanVcfParam-class ScanVcfParam,missing-method
> ###   ScanVcfParam,ANY-method vcfFixed vcfFixed<- vcfInfo vcfInfo<- vcfGeno
> ###   vcfGeno<- vcfSamples vcfSamples<- vcfTrimEmpty vcfTrimEmpty<-
> ###   vcfWhich vcfWhich<-
> ### Keywords: classes
> 
> ### ** Examples
> 
>   ScanVcfParam()
class: ScanVcfParam 
vcfWhich: 0 elements
vcfFixed: character() [All] 
vcfInfo:  
vcfGeno:  
vcfSamples:  
> 
>   fl <- system.file("extdata", "structural.vcf", package="VariantAnnotation")
>   compressVcf <- bgzip(fl, tempfile())
>   idx <- indexTabix(compressVcf, "vcf")
>   tab <- TabixFile(compressVcf, idx)
>   ## ---------------------------------------------------------------------
>   ## 'which' argument
>   ## ---------------------------------------------------------------------
>   ## To subset on genomic coordinates, supply an object 
>   ## containing the ranges of interest. These ranges can
>   ## be given directly to the 'param' argument or wrapped
>   ## inside ScanVcfParam() as the 'which' argument. 
> 
>   ## When using a list, the outer list names must correspond to valid
>   ## chromosome names in the vcf file. In this example they are "1" 
>   ## and "2".
>   gr1 <- GRanges("1", IRanges(13219, 2827695, name="regionA"))
>   gr2 <- GRanges(rep("2", 2), IRanges(c(321680, 14477080), 
+                  c(321689, 14477090), name=c("regionB", "regionC")))
>   grl <- GRangesList("1"=gr1, "2"=gr2)
>   vcf <- readVcf(tab, "hg19", grl)
> 
>   ## Names of the ranges are in the 'paramRangeID' metadata column of the
>   ## GRanges object returned by the rowRanges() accessor.
>   rowRanges(vcf)
GRanges object with 4 ranges and 5 metadata columns:
                                                                                     seqnames
                                                                                        <Rle>
                                                                     1:13220_T/<DEL>        1
  1:2827693_CCGTGGATGCGGGGACCCGCATCCCCTCTCCCTTCACAGCTGAGTGACCCACATCCCCTCTCCCCTCGCA/C        1
                                                                    2:321682_T/<DEL>        2
                                                           2:14477084_C/<DEL:ME:ALU>        2
                                                                                                   ranges
                                                                                                <IRanges>
                                                                     1:13220_T/<DEL> [   13220,    13220]
  1:2827693_CCGTGGATGCGGGGACCCGCATCCCCTCTCCCTTCACAGCTGAGTGACCCACATCCCCTCTCCCCTCGCA/C [ 2827693,  2827762]
                                                                    2:321682_T/<DEL> [  321682,   321682]
                                                           2:14477084_C/<DEL:ME:ALU> [14477084, 14477084]
                                                                                     strand
                                                                                      <Rle>
                                                                     1:13220_T/<DEL>      *
  1:2827693_CCGTGGATGCGGGGACCCGCATCCCCTCTCCCTTCACAGCTGAGTGACCCACATCCCCTCTCCCCTCGCA/C      *
                                                                    2:321682_T/<DEL>      *
                                                           2:14477084_C/<DEL:ME:ALU>      *
                                                                                     |
                                                                                     |
                                                                     1:13220_T/<DEL> |
  1:2827693_CCGTGGATGCGGGGACCCGCATCCCCTCTCCCTTCACAGCTGAGTGACCCACATCCCCTCTCCCCTCGCA/C |
                                                                    2:321682_T/<DEL> |
                                                           2:14477084_C/<DEL:ME:ALU> |
                                                                                     paramRangeID
                                                                                         <factor>
                                                                     1:13220_T/<DEL>      regionA
  1:2827693_CCGTGGATGCGGGGACCCGCATCCCCTCTCCCTTCACAGCTGAGTGACCCACATCCCCTCTCCCCTCGCA/C      regionA
                                                                    2:321682_T/<DEL>      regionB
                                                           2:14477084_C/<DEL:ME:ALU>      regionC
                                                                                                         REF
                                                                                              <DNAStringSet>
                                                                     1:13220_T/<DEL>                       T
  1:2827693_CCGTGGATGCGGGGACCCGCATCCCCTCTCCCTTCACAGCTGAGTGACCCACATCCCCTCTCCCCTCGCA/C CCGTGGATGC...TCCCCTCGCA
                                                                    2:321682_T/<DEL>                       T
                                                           2:14477084_C/<DEL:ME:ALU>                       C
                                                                                                 ALT
                                                                                     <CharacterList>
                                                                     1:13220_T/<DEL>           <DEL>
  1:2827693_CCGTGGATGCGGGGACCCGCATCCCCTCTCCCTTCACAGCTGAGTGACCCACATCCCCTCTCCCCTCGCA/C               C
                                                                    2:321682_T/<DEL>           <DEL>
                                                           2:14477084_C/<DEL:ME:ALU>    <DEL:ME:ALU>
                                                                                          QUAL
                                                                                     <numeric>
                                                                     1:13220_T/<DEL>         6
  1:2827693_CCGTGGATGCGGGGACCCGCATCCCCTCTCCCTTCACAGCTGAGTGACCCACATCCCCTCTCCCCTCGCA/C      <NA>
                                                                    2:321682_T/<DEL>         6
                                                           2:14477084_C/<DEL:ME:ALU>        12
                                                                                          FILTER
                                                                                     <character>
                                                                     1:13220_T/<DEL>        PASS
  1:2827693_CCGTGGATGCGGGGACCCGCATCCCCTCTCCCTTCACAGCTGAGTGACCCACATCCCCTCTCCCCTCGCA/C        PASS
                                                                    2:321682_T/<DEL>        PASS
                                                           2:14477084_C/<DEL:ME:ALU>        PASS
  -------
  seqinfo: 2 sequences from hg19 genome; no seqlengths
> 
>   ## which can be used for subsetting the VCF object
>   vcf[rowRanges(vcf)$paramRangeID == "regionA"]
class: CollapsedVCF 
dim: 2 1 
rowRanges(vcf):
  GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER
info(vcf):
  DataFrame with 10 columns: BKPTID, CIEND, CIPOS, END, HOMLEN, HOMSEQ, IMPR...
info(header(vcf)):
             Number Type    Description                                        
   BKPTID    .      String  ID of the assembled alternate allele in the asse...
   CIEND     2      Integer Confidence interval around END for imprecise var...
   CIPOS     2      Integer Confidence interval around POS for imprecise var...
   END       1      Integer End position of the variant described in this re...
   HOMLEN    .      Integer Length of base pair identical micro-homology at ...
   HOMSEQ    .      String  Sequence of base pair identical micro-homology a...
   IMPRECISE 0      Flag    Imprecise structural variation                     
   MEINFO    4      String  Mobile element info of the form NAME,START,END,P...
   SVLEN     .      Integer Difference in length between REF and ALT alleles   
   SVTYPE    1      String  Type of structural variant                         
geno(vcf):
  SimpleList of length 4: CN, CNQ, GQ, GT
geno(header(vcf)):
       Number Type    Description                                      
   CN  1      Integer Copy number genotype for imprecise events        
   CNQ 1      Float   Copy number genotype quality for imprecise events
   GQ  1      Float   Genotype quality                                 
   GT  1      String  Genotype                                         
>  
>   ## When using ranges, the seqnames must correspond to valid
>   ## chromosome names in the vcf file.
>   gr <- unlist(grl, use.names=FALSE)
>   vcf <- readVcf(tab, "hg19", gr)
>  
>   ## ---------------------------------------------------------------------
>   ## 'fixed', 'info', 'geno' and 'samples' arguments
>   ## ---------------------------------------------------------------------
>   ## This param specifies the "GT" 'geno' field for a single sample
>   ## and the subset of ranges in 'which'. All 'fixed' and 'info' fields 
>   ## will be returned. 
>   ScanVcfParam(geno="GT", samples="NA00002", which=gr)
class: ScanVcfParam 
vcfWhich: 2 elements
vcfFixed: character() [All] 
vcfInfo:  
vcfGeno: GT 
vcfSamples: NA00002 
>  
>   ## Here two 'fixed' and one 'geno' field are specified
>   ScanVcfParam(fixed=c("ALT", "QUAL"), geno="GT", info=NA) 
class: ScanVcfParam 
vcfWhich: 0 elements
vcfFixed: ALT, QUAL 
vcfInfo: NA 
vcfGeno: GT 
vcfSamples:  
> 
>   ## Return only the 'fixed' fields
>   ScanVcfParam(geno=NA, info=NA) 
class: ScanVcfParam 
vcfWhich: 0 elements
vcfFixed: character() [All] 
vcfInfo: NA 
vcfGeno: NA 
vcfSamples:  
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


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