Posts

Showing posts from March, 2016

Presence Absence Matrix

Given a cluster file, one can create a Presence-Absence matrix (PA map). With this self-explanatory simple matlab file it is easy to create one.

Input Format:

Cluster file.xlsx:
(1) A  B  C  D
(2) A  A  A
(3) B C
(4) D D A

List File.xlsx:
A
B
C
D

Output: (of course, the output will have the file with only numbers printed)

     A B C D
(1) 1  1  1  1
(2) 1  0  0  0
(3) 0  1  1  0
(4) 1  0  0  1



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26%Author = Arun Prasanna%Create a presence absence matrix (PA map) from cluster informationclear;clc;[mat1,mat]=xlsread('ClusterFile.xlsx','Sheet1');clearmat1[mat2,head]=xlsread('List.xlsx','Header');clearmat2new_head=head(:,col_val);%col_val = 2 => column that has unique sp/gene list[rmat,cmat]=size(mat);[rhead,chead]=size(new_head);out=zeros(rhead,rmat);fori=1:rheadforj=1:rmatfork=1:cmatcmp=strcmp(new_head(i,1),mat(j,k));if(cmp==1)out(i,j)=1;break;endendendendOF=xlswrite('Cluster…

Gene Copy Number Matrix

Given a cluster file, one can create a gene copy number matrix (GCN). With this self-explanatory simple matlab file it is easy to create one.
Input Format:
Cluster file.xlsx:
(1) A  B  C  D
(2) A  A  A
(3) B C
(4) D D A

List File.xlsx:
A
B
C
D

Output: (of course, the output will have the file with only numbers printed)

     A B C D
(1) 1  1  1  1
(2) 3  0  0  0
(3) 0  1  1  0
(4) 1  0  0  2


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29%Author = Arun Prasanna%Create a gene copy number matrix from cluster informationclear;clc;tic[mat1,mat]=xlsread('ClusterFile.xlsx','Sheet1');clearmat1[mat2,head]=xlsread('Organism_list.xlsx','Sheet1');clearmat2%species/gene namenew_head=head(:,1)';%transpose to make it as header[rmat,cmat]=size(mat);[rhead,chead]=size(new_head);out=zeros(rmat,chead);counter=0;fori=1:cheadi%print value of i to track progressforj=1:rmatfork=1:cmatcmp=strcmp(new_head(1,i),mat(j,k));chk=strcmp(mat…