Next-generation sequencing has revolutionized the study of cancer genomes. However, the tumor sample we obtained always consist of a mixture of normal and tumor tissue and the reads we get can be of multiple clonal types. MEpurity is a C++ program for calculating Tumor Purity using DNA methylation 450k data without matched normal control sample.
For more details about MEpurity, please visit the page Introduction of MEpurity.
To compile MEpurity you need two things: G++ (which usually are already installed on Linux) and Boost C++ Libraries. The last is not installed on Linux by default, but it can be downloaded from: Boostlib
Download the compressed source file MEpurity.tar.gz and do as follows:
$ tar -xzvf MEpurity.tar.gz
$ cd ./MEpurity/src
$ g++ bmm.cpp file.cpp help.cpp kmeans.cpp -o MEpurity -I [path-to-boostlib]/include/
Version 0.1
./MEpurity [options]
-f: The Illumina Infinium Human Methylation 450K (450k) input data.
-m: The normal mapfile under path of this software.
-o: The output file path that you would like to contain the results.
-h Show this help message and exit.
-s The number of CpG sites that you want to use in the map file. <int> (Default:80000)
-i: The Illumina Infinium Human Methylation 450K (450k) input data.
-p: The file under the path of the software (parameters.txt) that stores the parameters about the distribution of beta values at different CpG sites in normal samples.
-o: The output file path that you would like to contain the results.
-h Show this help message and exit.
-s The number of CpG sites that you want to use in the map file. <int> (Default:70000)
-t The maximum iteration time of bmm algorithm. <int> (Default:10000)
-c The least percemtage of sites belonging to a cluster that would not be filted. <float> (Default:0.01)
-n The original number of clusters. <int> (Default:10)
-v Output progress in terms of mixing coefficient (expected) values if 1. <bool> (Default:False)
./MEpurity -f ../test/test.txt -m ../map.txt -o ./output.txt
tar -zxvf ../test/test.tar.gz -C ../test
./MEpurity -i ../test/test.txt -p ../parameters.txt -o ./output.txt
The output file contains 2 columns:
1.Sample id
2.Tumor purity value