R: AA - amino acid table

AA {protViz} | R Documentation

## AA - amino acid table

### Description

Among other attributes it contains '1-letter code', 'monoisotopic mass' and 'average mass' of each amino acids.

### Format

contains a table

### Value

returns a `data.frame`

### Author(s)

Christian Panse 2013

### See Also

- http://www.matrixscience.com/help/aa_help.html

- http://education.expasy.org/student_projects/isotopident/htdocs/aa-list.html

- http://www.unimod.org

### Examples

        data(AA)
        AA
        AA.lm<-lm(AA$Monoisotopic ~ AA$Average)

        plot(AA$Monoisotopic, AA$Average);
        abline(AA.lm, col='grey')
        text(AA$Monoisotopic, AA$Average, AA$letter1, pos=3)

        plot(AA$Average-AA$Monoisotopic)
        axis(3,1:20,AA$letter1);
        abline(v=1:20,col='grey')

        # computes monoisotopic mass out of formula using the CDK package
        ## Not run:
        	if (require(rcdk)){
    	plot(AA$Monoisotopic,
    	     sapply(AA$formula, function(x){
    		     get.formula(as.character(x), charge = 1)@mass
    	     }))
    	}

    ## End(Not run)
        ## Not run:
    	    if (require(XML)){
    	unimodurl <- url("http://www.unimod.org/xml/unimod_tables.xml")
    	unimod.list <- XML::xmlToList(
    	  XML::xmlParse(
    	    scan(unimodurl, what = character())))
    	unimod.AA <- data.frame(
    	  do.call('rbind', unimod.list$amino_acids))
    	rownames(unimod.AA) <- unimod.AA$one_letter
    	    }

    ## End(Not run)

[Package protViz version 0.6.8 Index]