Normalize nucleotide counts.

Description

This functions performs a loess normalization of the nucleotide. This experimental feature can be used to compare experiments from different libraries or sequencing runs that may have differing noise characteristics.

Normalize nucleotide counts.

Normalize nucleotide counts.

Usage

normalize(test, control, ...)

## S4 method for signature 'matrix,matrix'
normalize(test, control, round=TRUE, ...)

## S4 method for signature 'deepSNV,missing'
normalize(test, control,  ...)

Arguments

Value

A deepSNV-class object.

Note

This feature is somewhat experimental and the results should be treated with care. Sometimes it can be better to leave the data unnormalized and use a model with greater dispersion instead.

Author(s)

Moritz Gerstung

Examples

data(phiX, package = "deepSNV")
plot(phiX)
phiN <- normalize(phiX, round = TRUE)
plot(phiN)

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(deepSNV)
Loading required package: parallel
Loading required package: Rhtslib
Rhtslib htslib version 1.1
Loading required package: IRanges
Loading required package: BiocGenerics

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: GenomicRanges
Loading required package: GenomeInfoDb
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: Biostrings
Loading required package: XVector
Loading required package: VGAM
Loading required package: splines
Loading required package: VariantAnnotation
Loading required package: Rsamtools

Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate


Attaching package: 'deepSNV'

The following objects are masked from 'package:VGAM':

    dbetabinom, pbetabinom

The following object is masked from 'package:BiocGenerics':

    normalize

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/deepSNV/normalize-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: normalize
> ### Title: Normalize nucleotide counts.
> ### Aliases: normalize normalize,deepSNV,missing-method
> ###   normalize,matrix,matrix-method
> 
> ### ** Examples
> 
> data(phiX, package = "deepSNV")
> plot(phiX)
> phiN <- normalize(phiX, round = TRUE)
> plot(phiN)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>