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.