Filtering criteria
- High confidence: at least 6 interleaved intrachromosomal SVs, 7 contiguous segments oscillating between 2 CN states, the fragment joins test, and either the chromosomal enrichment or the exponential distribution of breakpoints test.
- High confidence: at least 3 interleaved intrachromosomal SVs and 4 or more interchromosomal SVs, 7 contiguous segments oscillating between 2 CN states and the fragment joins test.
Filtering code
ssres2= ssres %>% mutate(high_conf = ((number_intra_SV>5 & max_number_oscillating_CN_segments_2_states>6 & pval_fragment_joins<0.01 & (chr_breakpoint_enrichment<0.01 | pval_exp_chr<0.01))) | ((number_intra_SV>3 & (inter_number_DEL+inter_number_h2hINV+inter_number_t2tINV+inter_number_DUP>4)) & pval_fragment_joins<0.01 & max_number_oscillating_CN_segments_2_states>6))
