List of tumor types

Description

Show all the possible tumor types accepted by LowMACA

Usage

showTumorType()

Details

This method is a wrapper around getCancerStudies and show all the barcodes for the tumor types as used by cBioPortal.

Value

A named vector of all the tumor types available in cgdsr package that can be passed to the method lmParams. Every element is the aggregation of all the available sequenced data from all the studies involved in a particular tumor type.

Author(s)

Stefano de Pretis , Giorgio Melloni

See Also

lmParams getCancerStudies

Examples

data('lmObj')
out <- showTumorType()
chosenTumors <- out[1:3]
lmParams(lmObj)$tumor_type <- chosenTumors

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)

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Type 'license()' or 'licence()' for distribution details.

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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(LowMACA)
Checking if clustalo is in the PATH...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
Can't locate XML/Simple.pm in @INC (you may need to install the XML::Simple module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .).
BEGIN failed--compilation aborted.
Warning messages:
1: In .ClustalChecks(ClustalCommand = "clustalo") :
  Clustal Omega is not in the PATH:
You can either change clustalo command using lmParams function or use the web service. See ?setup
2: running command '/usr/bin/perl -MXML::Simple -e 1' had status 2 
3: In .PerlModuleChecks(stop = FALSE, perl = "perl") :
  XML::Simple module for perl is not installed. 
            If you don't want to install a local clustal omega and use the web service, XML::Simple is required

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LowMACA/showTumorType.Rd_%03d_medium.png", width=480, height=480)
> ### Name: showTumorType
> ### Title: List of tumor types
> ### Aliases: showTumorType
> 
> ### ** Examples
> 
> data('lmObj')
> out <- showTumorType()
> chosenTumors <- out[1:3]
> lmParams(lmObj)$tumor_type <- chosenTumors
Warning message:
In `lmParams<-`(`*tmp*`, value = list(mutation_type = "missense",  :
  The path to clustal omega is not correct. Change it ore use the web service. See ?setup for details
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>