Correlation by lines in list

This software takes tables as input and computes the Pearson correlation coefficient 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 8 threads.

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.

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.

the executable file uses 8 threads per table. So if you set nb_cpu=4 the sofware will use 4x8=32 threads.

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')

8- you can use the command : perl parallel_format_table-0.1.pl to obtain a correlation table with means and SD.