MethylSig: Differential Methylation Testing for WGBS and RRBS Data

Documentation for package ‘methylSig’ version 0.99.4

bsseq_destranded	BSseq object read from destranded coverage files
bsseq_multichrom	BSseq object with loci on multiple chromosomes
bsseq_stranded	BSseq object read from stranded coverage files
diff_binomial	Differential methylation analysis using binomial model
diff_dss_fit	Performs model fit for general experimental design
diff_dss_test	Calculates differential methylation statistics under general experimental design
diff_methylsig	Calculates differential methylation statistics using a Beta-binomial approach
filter_loci_by_coverage	Filter BSseq object by coverage
filter_loci_by_group_coverage	Filter loci based on coverage threshold per sample per group
filter_loci_by_location	Remove loci by overlap with a 'GRanges' object
promoters_gr	GRanges object with collapsed promoters on chr21 and chr22
tile_by_regions	Group cytosine / CpG level data into regions based on genomic regions
tile_by_windows	Group cytosine / CpG level data into regions based on genomic windows