Working algos for Biological Data: Simple to Complex problems

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 information clear ; clc ; [ mat1 , mat ] = xlsread ( 'ClusterFile.xlsx' , 'Sheet1' ); clear mat1 [ mat2 , head ] = xlsread ( 'List.xlsx' , 'Header' ); clear mat2 new_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 ); for

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 information clear ; clc ; tic [ mat1 , mat ] = xlsread ( 'ClusterFile.xlsx' , 'Sheet1' ); clear mat1 [ mat2 , head ] = xlsread ( 'Organism_list.xlsx' , 'Sheet1' ); clear mat2 %species/gene name new_head = head (:, 1 ) ' ; %transpose to make it as header [ rmat , cmat ] = size ( mat ); [ rhead , chead ] = size ( new_head ); out = zeros ( rmat , chead );