Retrieve mutation data for a LowMACA object

Description

Exploting the capabilities of the cgdsr package, this method downloads and parse the mutation data of the specified genes in the selected tumor types. It also aggregates and show the frequencies of mutations of every gene in the different tumor types.

Usage

getMutations(object, repos = NULL)

Arguments

Details

With repos=NULL, the method is a wrapper around getMutationData method from package cgdsr-package. The output of the method is moduled by the parameters in lmParams("LowMACA_object"). See lmParams for further information.

Value

An object of class LowMACA is returned with an update in the slot mutations. See lmMutations method.

Author(s)

Stefano de Pretis , Giorgio Melloni

See Also

lmParams getMutationData lmMutations

Examples

#Create an object of class LowMACA
lm <- newLowMACA(pfam="PF12906")
#Change some paramters
#By default, LowMACA retrieve only missense mutations.
#We want all mutations
lmParams(lm)[['mutation_type']] <- 'all'
#By default, LowMACA takes mutations from all the kinds of tumor
#We want just prostate cancer samples
lmParams(lm)[['tumor_type']] <- 'prad'
lm <- getMutations(lm)

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(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/getMutations.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getMutations
> ### Title: Retrieve mutation data for a LowMACA object
> ### Aliases: getMutations
> 
> ### ** Examples
> 
> #Create an object of class LowMACA
> lm <- newLowMACA(pfam="PF12906")
> #Change some paramters
> #By default, LowMACA retrieve only missense mutations.
> #We want all mutations
> lmParams(lm)[['mutation_type']] <- 'all'
Warning message:
In `lmParams<-`(`*tmp*`, value = list(mutation_type = "all", tumor_type = "all_tumors",  :
  The path to clustal omega is not correct. Change it ore use the web service. See ?setup for details
> #By default, LowMACA takes mutations from all the kinds of tumor
> #We want just prostate cancer samples
> lmParams(lm)[['tumor_type']] <- 'prad'
Warning message:
In `lmParams<-`(`*tmp*`, value = list(mutation_type = "all", tumor_type = "prad",  :
  The path to clustal omega is not correct. Change it ore use the web service. See ?setup for details
> lm <- getMutations(lm)
Getting mutations from cancers studies...
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>