byzhang23/cross_species_conservation

Cross-species conservation

This is a repository for calculating cross-species conservation score. Here's a description of scripts:

• 1-1annotate_dhs_pairs.R: compile and annotate human/mouse DHS pairs
• 1-2preprocess_data.R: retain matched samples with anchor score > 0.5 and obtain the human/mouse normalized matrix for conservation score calculation
• 1-3split_annot.R: split the annotation files into smaller chunks
• 1-4get_coordinate.R: get coordinates
• 2compute_stat.R: calculate conservation scores for human-mouse DHS pairs
• 3null.R: construct a null distribution for each DHS pair category (9)
• 4-1compute_pvalue.R: calculate p-value
• 4-2compute_fdr_joint.R: combine all 9 categories and calculate FDR
• 5result_bygene.R: split the results by gene
• cnsv_score.R: core functions for calculating conservation scores