Enveomics collection

A toolbox for microbial genomics and metagenomics

Table.df2dist.R

Transform a tab-delimited list of distances into a squared matrix.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

§ Usage

Table.df2dist.R --x in_file [opts] out_file

§ Arguments

Input list*
 --x in_file  A tab-delimited table with the distances.
Obj1 index
 --obj1-index integer  Index of the column containing the ID of the object 1.
Obj2 index
 --obj2-index integer  Index of the column containing the ID of the object 2.
Dist index
 --dist-index integer  Index of the column containing the distance.
Default d
 --default-d integer  Default value for missing values. NA if empty.
Max sim
 --max-sim float  If not-empty, assumes that the values are similarity (not distance) and this is the maximum similarity (corresponding to distance 0). Applies transformation: distance = (max.sim - values)/max.sim.
Output file*
 out_file  Output squared matrix in tab-separated values format.
* Mandatory.