Functions used for making breaks and joins of the assembly
Functions for correctiong out-of-phase heterozygous SNPs.
Functions used for filtering and genotype calling from pbsv output.
Exampe of how to use pb_SV_analysis_functions.r
to filter and call genotypes
Does pairwise comparisons of methylation from allC files for a given set of regions and outputs to a file; results include per-sample number of methylated reads, unmethylated reads, and weighted methylation for each region
Computes the one-sided z-test pairwise between branches to identify significant differences in methylation. Uses the result of dmr_counts_pe.py
as the input
Assigns genomic feature to regions
Filter regions based on read coverage and number of covered positions in the region; remaining regions were used to determine methylation pseudo-alleles
Determine the methylation haplotype of regions for a given sample