R help - Dec 2015 - Looping through multiple sub elements of a list to compare to multiple components of a vector

I think I am making this problem harder than it has to be and so I keep getting
stuck on what might be a trivial problem.?
I have used the seqinr package to load a protein sequence alignment containing
15 protein sequences;
? ? > library(seqinr)? ? > x =
read.alignment("proteins.fasta",format="fasta",forceToLower=FALSE)This
automatically loads in a list of 4 elements including the sequences and other
information.
I store the sequences to a new list;
? ?> mylist = x$seqwhich returns a character vector of 15 strings.
I have found that if I split the long character strings into individual
characters it is easy to use lapply to loop over this list. So I use strsplit;
? ? >list.2 = strsplit(mylist, split = NULL)
>From this list I can determine which proteins have changes at certain
positions by using;
? ? >lapply(list.2, "[", 10) == "L"This returns a logical
T/F vector for those elements of the list that do/do not the letter L at
position 10.?
Because each of the protein sequences contains 99amino acids, I want to automate
this process so that I do not have to compare/contrast positions 1 x 1. Most of
the changes occur between positions/letters 10-95. I have a standard character
vector that I wish to use for comparison when looping through the list.?
Should I perhaps combine all -- ?the standard "letter"/aa vector, the
list of protein sequences -- into one list? Or is it better to leave them
separate for this comparison? I'm not sure what the output should be as I
need to use it for another statistical test. Would a list of logical vectors be
the most sufficient output to return??
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First, a couple posting tips.  It's helpful to provide some example data
people can work with.  Also, please post in plain text (not html).

If you have a single standard for comparison, you might find an approach
like this helpful.

# example data
mylist <- c("AAEBCC", "AABDCC", "AABBCD")
list.2 <- strsplit(mylist, split=NULL)

# setting a standard for comparison
std.string <- "AABBCC"
standard <- unlist(strsplit(std.string, split=NULL))

sapply(list.2, function(x) x==standard)

This gives you a matrix of logicals with the number of rows the same length
as your original strings (the 99 amino acids) and the number of columns the
same length as the number of strings you're comparing (the 15 sequences).

      [,1]  [,2]  [,3]
[1,]  TRUE  TRUE  TRUE
[2,]  TRUE  TRUE  TRUE
[3,] FALSE  TRUE  TRUE
[4,]  TRUE FALSE  TRUE
[5,]  TRUE  TRUE  TRUE
[6,]  TRUE  TRUE FALSE

Jean

On Wed, Dec 2, 2015 at 9:39 AM, debra ragland via R-help <
r-help at r-project.org> wrote:
> I think I am making this problem harder than it has to be and so I keep
> getting stuck on what might be a trivial problem.
> I have used the seqinr package to load a protein sequence alignment
> containing 15 protein sequences;
>     > library(seqinr)    > x >
read.alignment("proteins.fasta",format="fasta",forceToLower=FALSE)This
> automatically loads in a list of 4 elements including the sequences and
> other information.
> I store the sequences to a new list;
>    > mylist = x$seqwhich returns a character vector of 15 strings.
> I have found that if I split the long character strings into individual
> characters it is easy to use lapply to loop over this list. So I use
> strsplit;
>     >list.2 = strsplit(mylist, split = NULL)
> >From this list I can determine which proteins have changes at certain
> positions by using;
>     >lapply(list.2, "[", 10) == "L"This returns a
logical T/F vector for
> those elements of the list that do/do not the letter L at position 10.
> Because each of the protein sequences contains 99amino acids, I want to
> automate this process so that I do not have to compare/contrast positions 1
> x 1. Most of the changes occur between positions/letters 10-95. I have a
> standard character vector that I wish to use for comparison when looping
> through the list.
> Should I perhaps combine all --  the standard "letter"/aa vector,
the list
> of protein sequences -- into one list? Or is it better to leave them
> separate for this comparison? I'm not sure what the output should be as
I
> need to use it for another statistical test. Would a list of logical
> vectors be the most sufficient output to return?
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>
> ______________________________________________
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> PLEASE do read the posting guide
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> and provide commented, minimal, self-contained, reproducible code.
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