Convert chromosome into numeric values

Description

Convert chromosome into numeric values.

Usage

ChrNumeric(Chromosome)

Arguments

Details

For sexual chromosome, labels must contains X or Y which are coded by 23 and 24 respectively.

Note

People interested in tools dealing with array CGH analysis can visit our web-page http://bioinfo.curie.fr.

Author(s)

Philippe Hupé, glad@curie.fr

Examples

Chromosome <- c("1","X","Y","chr X", "ChrX", "chrX", "Chr   Y")
ChrNumeric(Chromosome)

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(GLAD)

######################################################################################

Have fun with GLAD

For smoothing it is possible to use either
the AWS algorithm (Polzehl and Spokoiny, 2002,
or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics,  2008,

If you use the package with AWS, please cite:
Hupe et al. (Bioinformatics, 2004, and Polzehl and Spokoiny (2002,

If you use the package with HaarSeg, please cite:
Hupe et al. (Bioinformatics, 2004, and (Ben-Yaacov and Eldar, Bioinformatics, 2008,

For fast computation it is recommanded to use
the daglad function with smoothfunc=haarseg

######################################################################################

New options are available in daglad: see help for details.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GLAD/ChrNumeric.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ChrNumeric
> ### Title: Convert chromosome into numeric values
> ### Aliases: ChrNumeric
> ### Keywords: manip
> 
> ### ** Examples
> 
> 
> Chromosome <- c("1","X","Y","chr X", "ChrX", "chrX", "Chr   Y")
> ChrNumeric(Chromosome)
[1]  1 23 24 23 23 23 24
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>