[R] More than on loop??

[che]

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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