nullProfile is a method for objects of class LowMACA
that draw a barplot highlighting the significant clusters
of mutations found by LowMACA statistics
a numeric value in the range of 0-1 that defines
the threshold of trident conservation score to include the specified position.
The default value is inherited from the slot entropy, whose default is 0.1
windowlimits
A vector indicating which amino acids residues will be
plotted. The vector refers to the positions in the global
alignment. By default this parameter is set to NULL,
that means that all the amino acids will be displayed.
Details
This method draw the second layer of the lmPlot of LowMACA.
The blue dotted line is a curve that pass through all the points of
the upper limit of the 95% confidence interval for the single position
test performed by entropy (one point per position in the consensus).
The black bars represents the density of mutations in our sample.
If a bar passes the blue line, it will be depicted in orange (significant pvalue).
After the correction for multiple testing, red stars appears at the top of the orange bars
if a cluster is below 0.05 for the qvalue and has a conservation trident score of at least 0.1.
Value
NULL
Author(s)
Stefano de Pretis , Giorgio Melloni
See Also
lmPlotentropy
Examples
#Load homeobox example
data(lmObj)
#Calculate statistics
lmObj <- entropy(lmObj)
nullProfile(lmObj)
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/nullProfile.Rd_%03d_medium.png", width=480, height=480)
> ### Name: nullProfile
> ### Title: Draw a mutational profile plot
> ### Aliases: nullProfile
>
> ### ** Examples
>
> #Load homeobox example
> data(lmObj)
> #Calculate statistics
> lmObj <- entropy(lmObj)
Making uniform model...
Assigned bandwidth: 0
> nullProfile(lmObj)
>
>
>
>
>
> dev.off()
null device
1
>