User Constructor for class

Description

User Constructor for class

Usage

ReadGoldData(genome, vcffilename, goldparams)

Arguments

Value

Object of class GoldData

Examples

gparam <-  GoldDataParam(percent.confirmed=0.792, percent.het.rare = 0.93)
g1000fn <- system.file("ext-data", "example_gold_file.vcf", package="genotypeeval")
g1000 <- ReadGoldData("GRCh38", g1000fn, gparam)

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.
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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(genotypeeval)
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

Warning message:
replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'genotypeeval' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/genotypeeval/ReadGoldData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ReadGoldData
> ### Title: User Constructor for class
> ### Aliases: ReadGoldData
> 
> ### ** Examples
> 
> gparam <-  GoldDataParam(percent.confirmed=0.792, percent.het.rare = 0.93)
> g1000fn <- system.file("ext-data", "example_gold_file.vcf", package="genotypeeval")
> g1000 <- ReadGoldData("GRCh38", g1000fn, gparam)
 Gold Data Constructor ... Reading Gold Data in (can take awhile) 
Warning message:
In keepSeqlevels(vr, reg.chrs) :
  invalid seqlevels'1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', 'X', 'Y'were ignored
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>