Correlation by lines in list Pearson Spearman
This software takes tables as input and computes the Pearson and Spearman correlation coefficients between all rows in a list against all the other rows.
Manual :
The software was written in GO and compiled on linux 64 bits with n threads depending of the number of CPUs availables.
1- install Perl free programming language and GNU parallel.
2- unzip the software
3- copy your n tables in csv (TAB delimitated by default) files in the “data” directory.
DATA in rows
The tables must have at least 3 rows.
- first line of the table : columns names
- first column : rows names
- separator : TAB
- decimal separator : '.'
- the software accept 'NA' and 'NaN' in the table
4- Edit the /rowlist/rowlist.txt file and write one rowname per line.
5- Edit the parallel configuration file to set the max number of CPUs = max number of tables processed in parallel.
6- execute the software by the command : perl corr_by_lines-0.8.pl
7- processed file is in the “result” directory.
Caution : If you process a very large table, the table will be too large to be opened in a spreadsheet. To open the table in R, don't forget to skip the first line using : read.csv(file="file.csv", skip=1, header=F, sep = '\t')
To obtain a table instead of a list, unzip the format table zip file into the software directory. Use the non_square Julia program (Julia v1.1.1 must be installed) preferentially. To obtain a square matrix, use the square Julia program with caution because the final matrix will be very large with many NA for correlations that have not been calculated.