PART and PART-up
PART and PART-up
Requirements:
perl, JAVA, R and the R poibin package
(http://cran.r-project.org/web/packages/poibin/index.html)
This program has been tested only on Unix and Mac.
How to install:
1)Download a file
wget http://www.hgc.jp/~niiyan/PART/part.tar.gz
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.
(http://www.bioconductor.org/packages/2.3/bioc/html/DNAcopy.html)
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 part.pl paired.seg probe.tsv
perl part_up.pl tumor.seg normal.seg probe.tsv
2) If you change cutoff for aberrations (default: 0.5),
perl part.pl -c 0.6 paired.seg probe.tsv
perl part_up.pl -c 0.6 tumor.seg normal.seg probe.tsv
3) If you assumes that aberrations is less than the cutoff,
perl part.pl -l paired.seg probe.tsv
perl part_up.pl -l tumor.seg normal.seg probe.tsv
4) If you want to decrease the number of the counted probes,
perl part.pl -t 1000 paired.seg probe.tsv
perl part_up.pl -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.
Reference:
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
Contact:
Atsushi Niida aniida@ims.u-tokyo.ac.jp