Find best normal sample in database

Description

Function to find the best matching normal for a provided tumor sample.

Usage

findBestNormal(gatk.tumor.file, normalDB, pcs = 1:3, 
    num.normals = 1, ignore.sex = FALSE, verbose = TRUE)

Arguments

Value

Filename of the best matching normal.

Author(s)

Markus Riester

Examples

gatk.normal.file <- system.file("extdata", "example_normal.txt", 
    package="PureCN")
gatk.normal2.file <- system.file("extdata", "example_normal2.txt", 
    package="PureCN")
gatk.normal.files <- c(gatk.normal.file, gatk.normal2.file)
normalDB <- createNormalDatabase(gatk.normal.files)

gatk.tumor.file <- system.file("extdata", "example_tumor.txt", 
    package="PureCN")
gatk.best.normal.file <- findBestNormal(gatk.tumor.file, normalDB)

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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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(PureCN)
Loading required package: DNAcopy
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/PureCN/findBestNormal.Rd_%03d_medium.png", width=480, height=480)
> ### Name: findBestNormal
> ### Title: Find best normal sample in database
> ### Aliases: findBestNormal
> 
> ### ** Examples
> 
> gatk.normal.file <- system.file("extdata", "example_normal.txt", 
+     package="PureCN")
> gatk.normal2.file <- system.file("extdata", "example_normal2.txt", 
+     package="PureCN")
> gatk.normal.files <- c(gatk.normal.file, gatk.normal2.file)
> normalDB <- createNormalDatabase(gatk.normal.files)
Allosome coverage appears to be missing, cannot determine sex.
Allosome coverage appears to be missing, cannot determine sex.
> 
> gatk.tumor.file <- system.file("extdata", "example_tumor.txt", 
+     package="PureCN")
> gatk.best.normal.file <- findBestNormal(gatk.tumor.file, normalDB)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>