A/B compartments identification
TIPS:
Function: Identifying A/B compartments by MDPH (Methylation data based pca.hic).
Test data: pal_50k_mlg18.txt, pal_50k_mlg18.bed, pal_50k_mythl_lg18.txt/pal_gene_lg18.txt, Lachesis_group18.
Download link of test file: https://github.com/yangxy2/3Dgenome-file/tree/main/web_test_file.
Input data description:
Hi-C contact matrix file: No header; 3 columns, separated by tab; From left to right, each column represents bin1 id, bin2 id, interaction frequency;
BED file: No header; 4 columns, separated by tab; From left to right, each column represents chromosome name, start coordinate, end coordinate, bin id;
Methylation level file: No header; 5 columns, separated by tab; From left to right, each column represents chromosome name, bin id, average methylation level(CG), average methylation level(CHG), average methylation level(CHH);
Chromosome: chromosome name.
Output file description: 6 columns, separated by tab; From left to right, each column represents chromosome name, start coordinate, end coordinate, size, strand, score (>0 is A compartments, <0 is B compartments, NA means neither of them).
Test data: pal_50k_mlg18.txt, pal_50k_mlg18.bed, pal_50k_mythl_lg18.txt/pal_gene_lg18.txt, Lachesis_group18.
Download link of test file: https://github.com/yangxy2/3Dgenome-file/tree/main/web_test_file.
Input data description:
Hi-C contact matrix file: No header; 3 columns, separated by tab; From left to right, each column represents bin1 id, bin2 id, interaction frequency;
BED file: No header; 4 columns, separated by tab; From left to right, each column represents chromosome name, start coordinate, end coordinate, bin id;
Methylation level file: No header; 5 columns, separated by tab; From left to right, each column represents chromosome name, bin id, average methylation level(CG), average methylation level(CHG), average methylation level(CHH);
Chromosome: chromosome name.
Output file description: 6 columns, separated by tab; From left to right, each column represents chromosome name, start coordinate, end coordinate, size, strand, score (>0 is A compartments, <0 is B compartments, NA means neither of them).
