genes : vector of selected genes for the analysis in Hugo names format. NULL if mode="pfam".
pfam : vector of selected domains for the analysis in pfam ids format. NULL if mode="genes".
input : data.frame describing the input data as gene symbols, pfam ids, entrez ids,
envelope start and end of the domain relative to the
protein, name of the canonical protein in uniprot format, amino acidic sequence.
mode : character. automatically set by the constructor as either "pfam" or "genes".
If pfam=NULL then mode="genes", "pfam" otherwise.
params : named list of starting parameters for the LowMaca analysis. Call lmParams(object) to show default.
See lmParams for further details.
parallelize : named list of logicals. getMutations=FALSE is the default for the getMutations
method and makeAlignment=TRUE is the default for the alignSequences method.
See parallelize for further details.
alignment
Object of class "list" with 4 elements:
ALIGNMENT : data.frame of the result of the alignment.
Every row represents a position of a sequence and the relative mapping to the consensus sequence.
SCORE : list of two elements. DIST_MAT is a matrix of pairwise similarities
between sequences as described by clustalo. SUMMARY_SCORE is a dataframe
of summary descriptive statistics of the DIST_MAT matrix
CLUSTAL : an object of class AAMultipleAlignment from package Biostrings
df : a data.frame describing the consensus sequence, its per-position degree
of conservation and its mutations null profile density.
See entropy and lmPlot for further details
mutations
Object of class "list" with 3 elements:
data : data.frame derived from the query to the cBioPortal query, getMutationData
Every row represents a mutation stratified by position, gene and tumor type.
freq : data.frame of absolute frequency of mutation stratified by gene and tumor type.
aligned : matrix representing the number of mutations at every position in the consensus sequence
(columns) and in each original sequence (rows)
entropy
Object of class "list" with 5 elements:
bw : numeric value. user defined bandwidth for the function entropy
uniform : function that generate the uniform null profile
absval : numeric value. Shannon entropy of the mutation data profile according to the defined bandwidth
log10pval : numeric value. pvalue of the entropy test in -log10 scale
pvalue : numeric value. pvalue of the entropy test
#ANALYSIS OF SOME OF THE PROTEINS THAT SHARE THE HOMEOBOX DOMAIN
#Genes to analyze
Genes <- c("ADNP","ALX1","ALX4","ARGFX","CDX4","CRX"
,"CUX1","CUX2","DBX2","DLX5","DMBX1","DRGX"
,"DUXA","ESX1","EVX2","HDX","HLX","HNF1A"
,"HOXA1","HOXA2","HOXA3","HOXA5","HOXB1","HOXB3"
,"HOXD3","ISL1","ISX","LHX8")
#Pfam to analyze
Pfam <- "PF00046"
#Construct a new LowMACA object
lm <- newLowMACA(genes=Genes , pfam=Pfam)
#Change some parameters
lmParams(lm)[['tumor_type']] <- c("skcm" , "stad" , "ucec" , "luad" , "lusc" , "coadread" , "brca")
lmParams(lm)[['min_mutation_number']] <- 1
lmParams(lm)[['density_bw']] <- 0
#Run if you have clustalo installed
lm <- setup(lm)
#Calculate staistics
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-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: LowMACA-class
> ### Title: Class '"LowMACA"'
> ### Aliases: LowMACA-class alignSequences,LowMACA-method
> ### bpAll,LowMACA-method entropy,LowMACA-method
> ### getMutations,LowMACA-method lfm,LowMACA-method lmPlot,LowMACA-method
> ### mapMutations,LowMACA-method nullProfile,LowMACA-method
> ### parallelize,LowMACA-method parallelize<-,LowMACA-method
> ### lmAlignment,LowMACA-method lmMutations,LowMACA-method
> ### lmEntropy,LowMACA-method lmParams,LowMACA-method
> ### lmParams<-,LowMACA-method protter,LowMACA-method setup,LowMACA-method
> ### show,LowMACA-method lfmSingleSequence,LowMACA-method
> ### lmPlotSingleSequence,LowMACA-method
> ### Keywords: classes
>
> ### ** Examples
>
> #ANALYSIS OF SOME OF THE PROTEINS THAT SHARE THE HOMEOBOX DOMAIN
> #Genes to analyze
> Genes <- c("ADNP","ALX1","ALX4","ARGFX","CDX4","CRX"
+ ,"CUX1","CUX2","DBX2","DLX5","DMBX1","DRGX"
+ ,"DUXA","ESX1","EVX2","HDX","HLX","HNF1A"
+ ,"HOXA1","HOXA2","HOXA3","HOXA5","HOXB1","HOXB3"
+ ,"HOXD3","ISL1","ISX","LHX8")
> #Pfam to analyze
> Pfam <- "PF00046"
> #Construct a new LowMACA object
> lm <- newLowMACA(genes=Genes , pfam=Pfam)
All Gene Symbols correct!
> #Change some parameters
> lmParams(lm)[['tumor_type']] <- c("skcm" , "stad" , "ucec" , "luad" , "lusc" , "coadread" , "brca")
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
> lmParams(lm)[['min_mutation_number']] <- 1
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
> lmParams(lm)[['density_bw']] <- 0
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
> #Run if you have clustalo installed
> 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