Correlation by columns

This software takes tables as input and computes the Pearson correlation coefficient between all combinations of columns.

Manual :

The software was written in GO and compiled on linux 64 bits.

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 columns.

- first line of the table : columns names

- first column : rows names

- separator : TAB

- decimal separator : '.'

- the software accept 'NA' and 'NaN' in the table

5- Edit the parallel configuration file "conf.txt" to set the max number of CPUs = max number of tables processed in parallel. The number of CPUs used for Pearson calculation are automatically detected.

4- execute the software by the command : parallel_corr_by_cols-ncpus.pl

5- processed file is in the “result” directory.

6- To obtain the result matrix type : perl main_format_table-0.1.pl and the output will be in the table 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')