FIND A SPECIFIC ELEMENT WITHIN A LIST OF GENE SYMBOLS

Hello everybody,

Could anyone suggest to me which kind of function I can use to find a specifi element whithin a list of gene symbols? I tried to use find but I couldn't get what I needed. Probably, I didn't use this function in a proper way.

Thanks for your help

[darova]

PLease show sample data. Show the code you used. Show the result you want to expect

Be more specific

[darova]

What about strfind?

[darova]

or contains

[Sa]

Ok, Thanks a lot.

Can I write something like that:

index = find (contains(MOUSEMATLAB,'March5'))

in which MOUSEMATLAB is my list of gene symbols and March5 is the specific element that I'm looking for.

I tried to use it and I got this:

Did you mean:

>> index = find (contains(MOUSEMATLAB,'March5'));

I don't understand what it means.

Thanks

Answer 1

[Sa]

Probe Set ID Gene Symbol

1415670_at Copg1

1415671_at Atp6v0d1

1415672_at Golga7

1415673_at Psph

1415674_a_at Trappc4

1415675_at Dpm2

This is part of the list that I have. For instance, I need to find a specific gene symbol such as Copg1 and its corresponding probeset ID whithin this list.

Thanks

[darova]

Please use comments section. Don't produce answer

[Sa]

ok, sorry!

Answer 2

[darova]

Try this

A = readtable('data.txt','delimiter','\t')
GENE = table2array(A(:,2));         % convert to cell
ix = strfind(GENE, 'Copg1');        % search in each cell
ix = cellfun(@isempty,ix);          % find empty cells
A(~ix,1)                            % display ID

[Sa]

Ok, thanks.

I tried it but I didn't get what I need.

Here's what I got

A =

6×1 table

ProbeSetIDGeneSymbol

_________________________

{'1415670_at Copg1' }

{'1415671_at Atp6v0d1'}

{'1415672_at Golga7' }

{'1415673_at Psph' }

{'1415674_a_at Trappc4' }

{'1415675_at Dpm2' }

Variable index exceeds table dimensions.

[darova]

This please?

A = importdata('data.txt');
for i = 2:size(A,1)
    A1(i-1,:) = strsplit(A{i},' ');
end
ix = strfind(A1(:,2), 'Copg1'); % search in each cell
ix = cellfun(@isempty,ix);      % find empty cells
A1(~ix,:)                       % display ID

[darova]

String delimiter might be 'space'

Can't be 'space' and 'tab' ath the same time. How your data separated?

[Sa]

Hi,

Thanks a lot for your help.

When I try this script using the file data.txt (the one that you sent to me), the script works and I can get the result I need. Instead, when I try it using my file MOUSE.txt it doesn't work. Here is the ans I get:

Unable to perform assignment because the size of the left side is 1-by-2 and the size of the right side is

1-by-7.

I am wondering if I can use another type of file rather than txt. For instance, a file excel that I can import in matlab.

Thanks

[darova]

Another attempt

clc,clear

A = importdata('data.txt');
for i = 2:size(A,1)
    a = textscan(A{i},'%s');
    A1(i-1,:) = cat(2,a{:});
end
ix = strfind(A1(:,2), 'Copg1'); % search in each cell
ix = cellfun(@isempty,ix);      % find empty cells
A1(~ix,:)                       % display ID

• I am wondering if I can use another type of file rather than txt. For instance, a file excel that I can import in matlab.

Yes, you can. But don't think it changes something. You have 'tab' and 'space' as a separation symbols

[Sa]

Sorry but it doesn't work even this time. If I use the file MOUSE.txt, this is the ans I got:

Unable to perform assignment because the size of the left side is 1-by-2 and the size of the right side is

6-by-1. It is similar to the previous one. I don't understand what it means.

Instead, if I use a file .xlsx, I get this result:

ans =

0×2 empty cell array

Thanks a lot

[darova]

Can you please attach the data?

[Sa]

Hello,

Here is the data.

Thanks

[darova]

Try this

A = readtable('ShortMouseDatabase.xlsx');
gene = table2array(A(:,2));
n = strfind(gene,'Copg1');
ix = ~cellfun(@isempty,n);
A(ix,1)

[Sa]

It works and I can get the result, thanks a lot.

have you used table2array because to use strfind your data needs to be an arry?

What does (@isempty,n) mean? Why do you put ~ before cellfun?

[darova]

• have you used table2array because to use strfind your data needs to be an arry?

Exactly. strfind refused to take table

• What does (@isempty,n) mean? Why do you put ~ before cellfun?

strfind returns cell arra. Cell can be empty or has some number. Number means position of substr in a cell. Empty cell means that substr was not found. I want to find all cells that are not empty. isempty check if cell is empty and return 0 or 1 (1 - empty). ix is logical array (0 and 1) of length gene

'~' tilde symbol means logical NOT

>> a = [0 0 1 1 0 0]
a =
     0     0     1     1     0     0
>> ~a
ans =
     1     1     0     0     1     1

[Sa]

Thanks, I understand it better now.

Is n referred to each cell of the array?

[Walter Roberson]

A = readtable('data.txt','delimiter','\t');
A(contains(A{:,2}, 'Copg1'), 1)

[darova]

n is cell array to which function is applied

[darova]

What does it supposed to mean?

[Sa]

OK, perfect. Really, thanks a lot