[R] More than on loop??

[che]

Thank you very much for your help,

you have been excused to have a suspicion, but  dont worry i am not
cheating, it is not a home work, rather it is a pre-project task that i have
to deal with in order to prepare to my project, and i cant understand this
programming things alone, i tried my best but still i cant deal with it
properly, i am studying master and PhD in bioinformatics, and i need to
develop a good understanding of  programming languages. still a beginner but
i start to have some fears ... what ever you send me, i study it and know
exactly how it works, and believe me that can help a lot to develop my
skills. Moreover i am dealing with it in a very honesty way that does not
break any academic regulations. 

thanks again i will try what you sent me ..

Yours 

che wrote:
> 
> hello every one,
> 
> How to function more than one loop in R? I have the following problem to
> be solved with the a method of three loops, can you help me please?
> 
> The data is attached with this message.
> 
> The data is composed of two parts, cleaved (denoted by “cleaved”) and non
> cleaved (denoted by “noncleaved”). 
> • to access to the ith peptide, you can use X$Peptide[i]
> • to access to the ith label, you can use X$Label[i]
>  
> define a set of amino acids using string or other format if you want
> amino.acid<-"ACDEFGHIKLMNPQRSTVWY"
> define two matrices with initialised entries, one for cleaved  peptides
> and one for none-cleaved peptides
> • matrix(0,AA,mer),where AA is the number of amino acids, and mer is the
> number
> of residues detected from data using the nchar function
> • both matrices have the same size, the number of rows being equal to the
> number
> of amino acids and the number of columns being equal to the number of
> residues
> in peptides
> 
> 
>  use one three-loop structure to detect the frequency of amino acids in
> cleaved peptides
> and one three-loop structure to detect the frequency of amino acids in
> non-cleaved
> peptides. They should not be mixed in one three-loop structure. The best
> way to
> handle this is to use a function. The three-loop structure is exampled as
> below
> for(i in 1:num)#scanning data for all peptides, where num means the number
> of peptides
> {
> for(j in 1:mer)#scanning all residues in a peptide
> {
> for(k in 1:AA)#scanning 20 amino acids
> {
> #actions
> }
> }
> }
>  http://n4.nabble.com/file/n1015851/hiv.dat hiv.dat 
> 

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