LowMACA : Low frequency Mutations Analysis via Consensus Alignment

Description

The LowMACA package is a simple suite of tools to investigate and analyze the mutation profile of several proteins or pfam domains via consensus alignment. You can conduct an hypothesis driven exploratory analysis using our package simply providing a set of genes or pfam domains of your interest.

Details

LowMACA allows to collect, align, analyze and visualize mutations from different proteins or pfam domains.

1. newLowMACA: construct a LowMACA object with your proteins or pfam

2. setup: align sequences, get mutations and map mutations on the consensus sequence

3. entropy: calculate entropy score and pvalues for every position

4. lfm: retrieve significant position

5. lmPlot: visualize mutations on the consensus sequence, conservation and significant clusters

Author(s)

Stefano de Pretis , Giorgio Melloni

Maintainer: <ste.depo@gmail.com> <melloni.giorgio@gmail.com>

References

Melloni GEM, de Pretis S, Riva L, et al. LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer. BMC Bioinformatics. 2016;17:80. doi:10.1186/s12859-016-0935-7

See Also

LowMACA project website

Examples

#Create an object of class LowMACA for RAS domain family
lm <- newLowMACA(pfam="PF00071" , genes=c("KRAS" , "NRAS" , "HRAS"))
#Select melanoma, breast cancer and colorectal cancer
lmParams(lm)$tumor_type <- c("skcm" , "brca" , "coadread")
#Align sequences, get mutation data and map them on consensus
lm <- setup(lm)
#Calculate statistics
lm <- entropy(lm)
#Retrieve original mutations
lfm(lm)
#Plot
bpAll(lm)
lmPlot(lm)
protter(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/LowMACA-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: LowMACA-package
> ### Title: LowMACA : Low frequency Mutations Analysis via Consensus
> ###   Alignment
> ### Aliases: LowMACA-package LowMACA
> ### Keywords: package
> 
> ### ** Examples
> 
> #Create an object of class LowMACA for RAS domain family
> lm <- newLowMACA(pfam="PF00071" , genes=c("KRAS" , "NRAS" , "HRAS"))
All Gene Symbols correct!
> #Select melanoma, breast cancer and colorectal cancer
> lmParams(lm)$tumor_type <- c("skcm" , "brca" , "coadread")
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
> #Align sequences, get mutation data and map them on consensus
> lm <- setup(lm)
Aligning sequences...
Error in .clustalOAlign(genesData, clustal_cmd, clustalo_filename, mail,  : 
  Clustal Omega command not found. clustalo is not in your PATH or it was not installed
Calls: setup ... setup -> alignSequences -> alignSequences -> .clustalOAlign
Execution halted