MethylSig: Differential Methylation Testing for WGBS and RRBS Data


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Documentation for package ‘methylSig’ version 0.99.4

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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