matrix

The gamtools matrix tool is used to calculate proximity matrices from segregation tables.

Usage and option summary

Usage:

gamtools matrix [OPTIONS] -s <SEGREGATION_FILE> -r <REGION> [<REGION> ...]

Optional parameters:

Option	Description
-f, –output-format	Output matrix file format (choose from: csv.gz, txt.gz, npz, txt, csv, png, default is txt.gz)
-t, –matrix-type	Method used to calculate the interaction matrix (choose from: cosegregation, linkage, dprime, npmi, default is npmi)
-o, –output-file	Output matrix file. If not specified, new file will have the same name as the segregation file and an extension indicating the genomic region(s) and the matrix method

Specifying regions

The -r/–regions parameter allows the user to specify the specific genomic regions to calculate matrices for. If one region is specified, a matrix is calculated for that region against itself. If more than one region is specified, a matrix is calculated for each region against the other. Regions are specified using UCSC browser syntax, i.e. “chr4” for the whole of chromosome 4 or “chr4:100000-200000” for a sub-region of the chromosome.