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| calc_asm | Calculate ASM Score |
| calc_derivedasm | Calculate SNP-based ASM |
| calc_logodds | Calculate the log odds ratio |
| calc_score | Calculate score |
| calc_weight | Calculate Weight for ASM Score |
| DAMEfinder | DAMEfinder: Method to detect allele-specific methylation (ASM), and differential ASM from Bisulfite sequencing data in R. |
| dame_track | Plot score tracks |
| dame_track_mean | Plot means per group of score tracks. |
| empirical_pval | Calculate empirical region-level p-value |
| extractbams_output | extract_bams() output. |
| extract_bams | Detect allele-specific methylation from a bam file |
| find_dames | Find DAMEs |
| getMD | MDtag parser |
| get_tstats | Get t-Statistics |
| methyl_circle_plot | Draw methylation circle plot |
| methyl_circle_plotCpG | Draw methylation circle plot without SNP |
| methyl_MDS_plot | Multidimensional scaling plot of distances between methylation proportions (beta values) |
| modulus_sqrt | Get Modulus Square Root |
| readtuples_output | read_tuples() output. |
| read_tuples | Read in list of methtuple files |
| simes_pval | Calculate region-level p-value |
| splitReads | Divide read names by allele |