R: Generate a list of GRanges objects from a VCF file.
InputVcf
R Documentation
Generate a list of GRanges objects from a VCF file.
Description
The InputVcf() function generates a list of GRanges
object from a single VCF file.
Usage
InputVcf(vcfFile, ...)
Arguments
vcfFile
a character contains the path and name of
a VCF file
...
additional arguments
Details
Read all fields in a VCF file into GRanges object.
Value
a list of GRanges object containing a representation of
data from the VCF file
Author(s)
Xiaojing Wang
Examples
## multiple samples in one VCF file
vcffile <- system.file("extdata", "test_mul.vcf", package="customProDB")
vcfs <- InputVcf(vcffile)
length(vcfs)
## single sample
vcffile <- system.file("extdata/vcfs", "test1.vcf", package="customProDB")
vcf <- InputVcf(vcffile)
length(vcf)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(customProDB)
Loading required package: IRanges
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
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: AnnotationDbi
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: biomaRt
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/customProDB/InputVcf.Rd_%03d_medium.png", width=480, height=480)
> ### Name: InputVcf
> ### Title: Generate a list of GRanges objects from a VCF file.
> ### Aliases: InputVcf
>
> ### ** Examples
>
> ## multiple samples in one VCF file
>
> vcffile <- system.file("extdata", "test_mul.vcf", package="customProDB")
> vcfs <- InputVcf(vcffile)
> length(vcfs)
[1] 5
>
> ## single sample
>
> vcffile <- system.file("extdata/vcfs", "test1.vcf", package="customProDB")
> vcf <- InputVcf(vcffile)
> length(vcf)
[1] 1
>
>
>
>
>
> dev.off()
null device
1
>