PART and PART-up



perl, JAVA, R and the R poibin package


This program has been tested only on Unix and Mac.

How to install:

  1. 1)Download a file


2) Uncompress the file

tar xvzf part.tar.gz

the resulting  directory contains a README file, the "java" and "data" directories, and the  "part", and "part_up" perl scripts.

How to prepare input data:

PART and PART-up need segmented copy number or LOH data and SNP or CGH array probe information.

As examples, TCGA colorectal cancer LOH data are provided in the data directory.

1) A segment  file

This is a seg format file from the Circular Binary Segmentation algorithm.


2) A  probe information file

This is a tsv file containing probe ids, chromosome ids (1,2..24), coordinates on each chromosome, in the 1st, 2nd and 3rd columns respectively.

How to run:

1) A basic usage is:

perl  paired.seg probe.tsv

perl  tumor.seg  normal.seg probe.tsv

2) If you change cutoff for aberrations (default: 0.5),

perl -c 0.6  paired.seg probe.tsv

perl  -c 0.6 tumor.seg  normal.seg probe.tsv

3) If you assumes that aberrations is less than the cutoff,

perl -l  paired.seg probe.tsv

perl  -l tumor.seg  normal.seg probe.tsv

4) If you want to decrease the number of the counted probes,

perl -t 1000   paired.seg probe.tsv

perl  -t 1000 tumor.seg  normal.seg probe.tsv

These count one per every 1000 probes.

The result is printed out to the standard output.

Each line contains the probe id, chromosome, coordinate, p-value and q-value.


Niida, A and Imoto, S and Shimamura, T and Miyano, S

Statistical model-based testing to evaluate the recurrence of genomic aberrations

Bioinformatics, 2012, 28:i115-i120


Atsushi Niida