Differential methylation test using a binomial model
This function calculates differential methylation statistics using a binomial-based approach. It is nearly identical to the \code{methylKit::calculateDiffMeth} function in the \code{methylKit} R package except that the likelihood ratio test and \code{p.adjust(..., method = 'BH')} are used to calculate significance levels. It is significantly faster than \code{methylKit::calculateDiffMeth} function.
Arguments
bs a BSseq object possibly having passed through prior filtering and tiling functions.
group_column a character string indicating the column of pData(bs) to use to determine group membership.
comparison_groups a named character vector indicating the case and control factors of group_column for the comparison.
Values
A GRanges corresponding to loci tested with extra mcols:
Function call
diff_binomial(bs, group, case, control)Description
Differential methylation test using a binomial model
This function calculates differential methylation statistics using a binomial-based approach. It is nearly identical to the \code{methylKit::calculateDiffMeth} function in the \code{methylKit} R package except that the likelihood ratio test and \code{p.adjust(..., method = 'BH')} are used to calculate significance levels. It is significantly faster than \code{methylKit::calculateDiffMeth} function.
Arguments
bsaBSseqobject possibly having passed through prior filtering and tiling functions.group_columnacharacterstring indicating the column ofpData(bs)to use to determine group membership.comparison_groupsa namedcharactervector indicating thecaseandcontrolfactors ofgroup_columnfor the comparison.Values
A
GRangescorresponding to loci tested with extramcols:Tests
Test for correct return forms.