DMRcate-package |
DMR calling from bisulfite sequencing and Illumina array data |
changeFDR |
Change the individual CpG FDR thresholding for a CpGannotated object. |
cpg.annotate |
Annotate Illumina CpGs with their chromosome position and test statistic |
CpGannotated-class |
An object summarising individual CpG sites fitted to a given model |
DMR.plot |
Plotting DMRs |
DMRcate |
DMR calling from bisulfite sequencing and Illumina array data |
dmrcate |
DMR identification |
DMResults-class |
Initial storage object for called DMRs - class |
extractRanges |
Create a GRanges object from 'dmrcate' output. |
plot |
Plotting DMRs |
rmPosReps |
Filter out position replicates from an EPICv2 beta- or M-matrix |
rmSNPandCH |
Filter probes |
sequencing.annotate |
Annotate a bisulfite sequencing experiment (WGBS or RRBS) with probe weights and chromosomal position. |