How can I create a function which takes a matrix of characters as the input and outputs the number of specific characters within that matrix?

I am looking for a function, not an equation or anything else that may be simpler.

I have the following sequence (matrix)

bases = [ 't' 't' 'a' 'c' 'a' 'a' 't' 'g' 'g' 'a' 'g' 't' 'a' 'a' 'g';...
         'a' 'g' 't' 'a' 'a' 'c' 'c' 'a' 'c' 'g' 'c' 't' 'a' 't' 'c';...
         'a' 'c' 'c' 'c' 'g' 'g' 'a' 'a' 'a' 'a' 'a' 't' 'c' 'c' 'c';...
         'a' 'c' 'a' 't' 'c' 'c' 'c' 'c' 'c' 'c' 't' 't' 'g' 't' 'g' ]

I need the functuon to input a matrix like above but not specifically that matrix, that is just an example, it has to work for multiple sequences.

The output must be the number of 'gc' combinations within the sequence.

I have tried

function [ GCRatio ] = func3( B )
GCRatio = numel(strfind (B,'gc'))

end  

though this has not worked

[Stephen23]

See also earlier question and discussion:

https://www.mathworks.com/matlabcentral/answers/430955-how-can-i-create-a-for-loop-to-count-the-number-of-letters-in-my-array

Note that your matrix definition is equivalent to this:

bases = [...
    'ttacaatggagtaag';...
    'agtaaccacgctatc';...
    'acccggaaaaatccc';...
    'acatccccccttgtg']

"The output must be the number of 'gc' combinations within the sequence."

What does "combinations" mean exactly? Is the order significant? Can they overlap? Which of these would count as one/two/three sequences?:

gcgc % is this one or two?
cg   % is order significant?
gccg % ???
cgccg% one, two, or three?

[Fope Ayo]

combinations - by this i just mean the one combination of ‘gc’

gcgc %this is two
cg % non significant
gccg % non significant 
cgccg % this would equivalate to one gc sequence

[Fope Ayo]

sorry

gccg % this would = one

Answer 1

[Stephen23]

Two methods to count the exact sequence 'gc' on each line of the character matrix.

Method one: convert to cell array, use strfind and cellfun:

>> cellfun(@numel,strfind(num2cell(bases,2),'gc'))
ans =
   0
   1
   0
   0

It is easy to make this into a function:

>> fun = @(m)cellfun(@numel,strfind(num2cell(m,2),'gc'));
>> fun(bases)
ans =
   0
   1
   0
   0 

Method two: logical arrays and sum:

>> sum(bases(:,1:end-1)=='g' & bases(:,2:end)=='c',2)
ans =
   0
   1
   0
   0

This is also easy to make into a function:

>> fun = @(m) sum(m(:,1:end-1)=='g' & m(:,2:end)=='c',2);
>> fun(bases)
ans =
   0
   1
   0
   0

[Fope Ayo]

@(m)cellfun(@numel,strfind(num2cell(m,2),'gc'));

This is the equation overall, so in coding the function what exactly do I write?

function [ GCRatio ] = myfunction( bases )
GCRatio = @(m)cellfun(@numel,strfind(num2cell(m,2),'gc'));

[Stephen23]

"This is the equation overall, so in coding the function what exactly do I write?"

I already gave you two examples of functions, both named fun in my answer :

https://www.mathworks.com/help/matlab/matlab_prog/anonymous-functions.html

I do not know what you mean by "equation" in relation to the functions that I gave you.

You do not need to put those anonymous functions inside another function to use them: they are already functions, so you can just call them like any other function, using the name fun. I showed you this in my answer.

However if you really want to write a main/local/nested function, then just get rid of the anonymous function definition and call the cellfun directly:

function out = myfunction(m)
out = cellfun(@numel,strfind(num2cell(m,2),'gc'));
end

You can read about different function types here:

https://www.mathworks.com/help/matlab/matlab_prog/types-of-functions.html

[Fope Ayo]

Thank you